From 8c85a0874a5edd2c66181cd4f2f422fdd309426a Mon Sep 17 00:00:00 2001 From: Lauren Rekerle Date: Tue, 9 Jan 2024 10:28:30 -0600 Subject: [PATCH 01/25] updates to error messages --- ...tinez_PMID_36446582_RunGenoPhenoCorr.ipynb | 2351 ++++++++--------- .../preprocessing/_phenopacket.py | 30 +- src/genophenocorr/preprocessing/_phenotype.py | 6 +- 3 files changed, 1184 insertions(+), 1203 deletions(-) diff --git a/notebooks/KBG/KBG_Martinez_PMID_36446582_RunGenoPhenoCorr.ipynb b/notebooks/KBG/KBG_Martinez_PMID_36446582_RunGenoPhenoCorr.ipynb index cb5daa11..aa851192 100644 --- a/notebooks/KBG/KBG_Martinez_PMID_36446582_RunGenoPhenoCorr.ipynb +++ b/notebooks/KBG/KBG_Martinez_PMID_36446582_RunGenoPhenoCorr.ipynb @@ -85,256 +85,258 @@ "name": "stderr", "output_type": "stream", "text": [ - "Patients Created: 0%| | 0/328 [00:00\n", "ItemDescription\n", - "Description of the cohort. \n", - "Total Individuals251\n", + "Description of the cohort. 77 individuals were removed from the cohort because they had no HPO terms.\n", + "Total Individuals329\n", + "Excluded Individuals77: PMID_36446582_KBG58;PMID_36446582_Goldenberg2016_P19;PMID_36446582_Goldenberg2016_P3;PMID_36446582_Parenti2021_P23;PMID_36446582_Goldenberg2016_P26;PMID_36446582_Willemsen2010_P2;PMID_36446582_Novara,_2017_P11;PMID_36446582_Willemsen2010_P4;PMID_36446582_Novara,_2017_P12;PMID_36446582_Goldenberg2016_P13;PMID_36446582_Sacharow,_2012_P1;PMID_36446582_Scarano,_2013_P12;PMID_36446582_Goldenberg2016_P20;PMID_36446582_Goldenberg2016_P21;PMID_36446582_Gnazzo,_2020_P31;PMID_36446582_Bucerzan2020;PMID_36446582_KBG22;PMID_36446582_KBG2;PMID_36446582_Novara,_2017_P4;PMID_36446582_Crippa2015_P2;PMID_36446582_Khalifa,_2013_P1B;PMID_36446582_Gnazzo,_2020_P29;PMID_36446582_Goldenberg2016_P32;PMID_36446582_Kutkowska-Kazmierczak2021_P17;PMID_36446582_Ockeloen2015_P20;PMID_36446582_Kutkowska-Kazmierczak2021_P14;PMID_36446582_Kutkowska-Kazmierczak2021_P16;PMID_36446582_Goldenberg2016_P29;PMID_36446582_KBG25;PMID_36446582_Scarano,_2013_P10;PMID_36446582_Isrie,_2012_P1;PMID_36446582_Goldenberg2016_P2;PMID_36446582_Kutkowska-Kazmierczak2021_P23;PMID_36446582_Youngs2011;PMID_36446582_Goldenberg2016_P10;PMID_36446582_Goldenberg2016_P22;PMID_36446582_Spengler,_2013;PMID_36446582_KBG38;PMID_36446582_Willemsen2010_P1;PMID_36446582_Kutkowska-Kazmierczak2021_P19;PMID_36446582_Scarano,_2013_P11;PMID_36446582_KBG26;PMID_36446582_Novara,_2017_P3;PMID_36446582_Goldenberg2016_P4;PMID_36446582_Behnert,_2018;PMID_36446582_Kutkowska-Kazmierczak2021_P15;PMID_36446582_Kutkowska-Kazmierczak2021_P21;PMID_36446582_Goldenberg2016_P24;PMID_36446582_Isrie,_2012_P2;PMID_36446582_Goldenberg2016_P33;PMID_36446582_Willemsen2010_P3;PMID_36446582_KBG9;PMID_36446582_Palumbo_2016;PMID_36446582_Goldenberg2016_P36;PMID_36446582_Miyatake,_2013;PMID_36446582_Crippa2015_P3;PMID_36446582_Novara,_2017_P7;PMID_36446582_Srivastava,_2017_P1;PMID_36446582_Gnazzo,_2020_P30;PMID_36446582_Goldenberg2016_P1;PMID_36446582_Novara,_2017_P1;PMID_36446582_Goldenberg2016_P12;PMID_36446582_KBG1;PMID_36446582_Kutkowska-Kazmierczak2021_P18;PMID_36446582_Novara,_2017_P2;PMID_36446582_Goldenberg2016_P28;PMID_36446582_Kutkowska-Kazmierczak2021_P22;PMID_36446582_Lim2014;PMID_36446582_Novara,_2017_P8;PMID_36446582_Novara,_2017_P9;PMID_36446582_Goldenberg2016_P18;PMID_36446582_KBG23;PMID_36446582_Sacharow,_2012_P2;PMID_36446582_Kutkowska-Kazmierczak2021_P20;PMID_36446582_Novara,_2017_P5;PMID_36446582_Crippa2015_P1;PMID_36446582_Khalifa,_2013_P1A\n", "Total Unique HPO Terms27\n", - "Total Unique Variants251\n", + "Total Unique Variants252\n", "" ], "text/plain": [ @@ -461,16 +464,16 @@ "\n", "\n", "\n", - "\n", + "\n", "\n", "\n", "\n", "\n", "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", "\n", "\n", @@ -535,36 +538,36 @@ "\n", "\n", "\n", + "\n", "\n", - "\n", - "\n", "\n", - "\n", - "\n", - "\n", + "\n", "\n", - "\n", - "\n", + "\n", "\n", "\n", - "\n", + "\n", + "\n", + "\n", + "\n", "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", + "\n", "\n", + "\n", + "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "\n", + "\n", + "\n", + "\n", + "\n", + "\n", "
HPO TermCount
Counts of annotations to HPO terms for the 251 in the cohortCounts of annotations to HPO terms for the 329 in the cohort
Macrodontia (HP:0001572)182
Intellectual disability (HP:0001249)159
Abnormality of the hand (HP:0001155)156
Global developmental delay (HP:0001263)133
Short stature (HP:0004322)115
Abnormal external nose morphology (HP:0010938)112
Thick eyebrow (HP:0000574)105
Thick eyebrow (HP:0000574)106
Long philtrum (HP:0000343)103
Hearing impairment (HP:0000365)74
Hearing impairment (HP:0000365)75
Triangular face (HP:0000325)68
Abnormality of the outer ear (HP:0000356)58
Attention deficit hyperactivity disorder (HP:0007018)51
VariantEffectCountKey
c.1903_1907delFRAMESHIFT_VARIANT3316_89284634_89284639_GTGTTT_G
c.2408_2412delFRAMESHIFT_VARIANT1016_89284129_89284134_CTTTTT_C
c.2398_2401delFRAMESHIFT_VARIANT916_89284140_89284144_TTTTC_T
c.1381_1384delFRAMESHIFT_VARIANT816_89285157_89285161_GTTTC_G
c.2398_2401delFRAMESHIFT_VARIANT816_89284140_89284144_TTTTC_T
c.6792_6793insCFRAMESHIFT_VARIANT516_89279749_89279749_C_CG
c.7481_7482insCFRAMESHIFT_VARIANT516_89275180_89275180_A_AG
c.2182_2183delFRAMESHIFT_VARIANT316_89284358_89284360_GAT_G
c.3832A>TSTOP_GAINED316_89282710_89282710_T_A
c.2197C>TSTOP_GAINED316_89284345_89284345_G_A
c.6792_6793insCFRAMESHIFT_VARIANT516_89279749_89279749_C_CG
c.7570-1G>CSPLICE_ACCEPTOR_VARIANT316_89274958_89274958_C_G
c.3224_3227delFRAMESHIFT_VARIANT316_89283314_89283318_CCTTT_C
c.1977C>GSTOP_GAINED316_89284565_89284565_G_C
c.3832A>TSTOP_GAINED316_89282710_89282710_T_A
c.2175_2178delFRAMESHIFT_VARIANT316_89284363_89284367_CTTTG_C
c.4406G>ASTOP_GAINED316_89282136_89282136_C_T
c.5790C>ASTOP_GAINED216_89280752_89280752_G_T
c.1977C>GSTOP_GAINED316_89284565_89284565_G_C
c.2197C>TSTOP_GAINED316_89284345_89284345_G_A
c.2182_2183delFRAMESHIFT_VARIANT316_89284358_89284360_GAT_G
c.3224_3227delFRAMESHIFT_VARIANT316_89283314_89283318_CCTTT_C
c.1367_1370delFRAMESHIFT_VARIANT216_89285171_89285175_CTTCT_C
c.4384_4385insAFRAMESHIFT_VARIANT216_89282157_89282157_C_CT
c.3309_3310insAFRAMESHIFT_VARIANT216_89283232_89283232_C_CT
c.2329_2332delFRAMESHIFT_VARIANT216_89284209_89284213_TTCTC_T
c.3045delFRAMESHIFT_VARIANT216_89283496_89283497_CG_C
c.5488G>TSTOP_GAINED216_89281054_89281054_C_A
c.3704_3707delFRAMESHIFT_VARIANT216_89282834_89282838_CTGTT_C
c.3590_3594delFRAMESHIFT_VARIANT216_89282947_89282952_CTTTTT_C
c.1318C>TSTOP_GAINED216_89285224_89285224_G_A
c.2329_2332delFRAMESHIFT_VARIANT216_89284209_89284213_TTCTC_T
c.3309_3310insAFRAMESHIFT_VARIANT216_89283232_89283232_C_CT
c.1385_1388delFRAMESHIFT_VARIANT216_89285153_89285157_TTTTG_T
c.4087C>TSTOP_GAINED216_89282455_89282455_G_A
c.7534C>TMISSENSE_VARIANT216_89275128_89275128_G_A
c.7216C>TSTOP_GAINED216_89279326_89279326_G_A
c.3590_3594delFRAMESHIFT_VARIANT216_89282947_89282952_CTTTTT_C
c.5790C>ASTOP_GAINED216_89280752_89280752_G_T
c.4087C>TSTOP_GAINED216_89282455_89282455_G_A
c.6513_6514insCFRAMESHIFT_VARIANT216_89280028_89280028_C_CG
c.3704_3707delFRAMESHIFT_VARIANT216_89282834_89282838_CTGTT_C
c.3045delFRAMESHIFT_VARIANT216_89283496_89283497_CG_C
c.4384_4385insAFRAMESHIFT_VARIANT216_89282157_89282157_C_CT
c.7216C>TSTOP_GAINED216_89279326_89279326_G_A
c.5488G>TSTOP_GAINED216_89281054_89281054_C_A
\n", "

Additionally, the following variants were observed 1 or fewer times: \n", - "c.5274_5275insC; c.2130del; c.5146G>T; c.3123_3126del; c.6015_6016insA; c.4528_4529del; c.6184del; c.3310_3311insG; c.3582del; c.6472G>T; c.2305del; c.211_226+1del; c.2593_2594insT; c.3974del; c.831del; c.7607G>A; c.6682del; c.6691_6692insG; c.3460G>T; c.2765_2766del; c.3448C>T; c.5145C>G; c.2866G>T; c.7000C>T; c.3339G>A; c.3153del; c.6053_6057del; c.4964_4965del; c.4171C>T; c.6628G>T; c.7535G>A; c.2647G>T; c.4558del; c.6409_6410del; c.4374_4375del; c.4283_4286del; c.4206C>G; c.5123C>A; c.1801C>T; c.3334del; c.2828_2829del; c.2512C>T; c.520C>T; c.6817_6833del; c.3221_3222del; c.3591_3594del; c.4391_4392del; c.2751_2752insT; c.1711_1723del; c.2692C>T; c.3771_3772insA; c.7407C>G; c.2297_2300del; c.3180_3181insA; c.3208_3209del; c.4498C>T; c.7356_7357insC; c.4218C>A; c.4107_4108del; c.7192C>T; c.5712_5713insT; c.2395A>T; c.548_551del; c.2650del; c.7552C>T; c.3437_3461del; c.5957_5958del; c.7471A>C; c.3774_3775del; c.1846G>T; c.3222_3223insA; c.1173C>G; c.6766C>T; c.4389_4390del; c.5205del; c.1457C>G; c.3046del; c.5199_5227del; c.7753C>T; c.3193A>T; c.5889del; c.1285_1286del; c.7570_7572del; c.505G>T; c.7180C>T; c.6968_6975del; c.1763C>A; c.7834G>T; c.866_867insA; c.1460_1463del; c.3888_3889insC; c.1940_1941delinsT; c.5953_5954del; c.6340C>T; c.2412del; c.7471-1G>C; c.7416C>G; c.1120G>T; c.6071_6084del; c.1785_1786delinsTT; c.3198_3199del; c.3019C>T; c.7189C>T; c.3770_3771del; c.3931C>T; c.4786G>T; c.7470+2T>C; c.3295_3296del; c.4103_4104del; c.5426_5430del; c.1893_1894insA; c.7363del; c.3905_3906del; c.1731_1732insT; c.5483C>A; c.4177_4189del; c.6364_6367del; c.867C>G; c.2367del; c.915del; c.1389_1390insA; c.6701del; c.3382_3383del; c.4529_4530insC; c.6187G>T; c.4408A>T; c.7411_7422del; c.7083del.

\n", + "c.7570_7572del; c.7607G>A; c.1460_1463del; c.5889del; c.5953_5954del; c.3931C>T; c.4528_4529del; c.915del; c.7471-1G>C; c.5146G>T; c.7535G>A; c.211_226+1del; c.1389_1390insA; c.2647G>T; c.4529_4530insC; c.831del; c.6968_6975del; c.2367del; c.3888_3889insC; c.3295_3296del; c.4218C>A; c.3460G>T; c.2512C>T; c.2765_2766del; c.3382_3383del; c.2866G>T; c.520C>T; c.3437_3461del; c.5199_5227del; c.7470+2T>C; c.7552C>T; c.7180C>T; c.3774_3775del; c.6364_6367del; c.5145C>G; c.4408A>T; c.6766C>T; c.3770_3771del; c.6184del; c.3974del; c.1846G>T; c.4171C>T; c.4206C>G; c.5205del; c.1731_1732insT; c.3046del; c.4103_4104del; c.5957_5958del; c.2297_2300del; c.866_867insA; c.2593_2594insT; c.7411_7422del; c.1120G>T; c.3334del; c.6472G>T; c.2751_2752insT; c.7471A>C; c.867C>G; c.7416C>G; c.5426_5430del; c.7000C>T; c.4498C>T; c.3123_3126del; c.6628G>T; c.2650del; c.1801C>T; c.3153del; c.7753C>T; c.7189C>T; c.6187G>T; c.4177_4189del; c.3193A>T; c.548_551del; c.3208_3209del; c.4391_4392del; c.3448C>T; c.3591_3594del; c.6015_6016insA; c.4107_4108del; c.2305del; c.6691_6692insG; c.1285_1286del; c.4374_4375del; c.3771_3772insA; c.3339G>A; c.1893_1894insA; c.505G>T; c.1457C>G; c.6071_6084del; c.6682del; c.1173C>G; c.5123C>A; c.3222_3223insA; c.2412del; c.2692C>T; c.3310_3311insG; c.4283_4286del; c.4786G>T; c.3180_3181insA; c.5483C>A; c.3905_3906del; c.7407C>G; c.7356_7357insC; c.6053_6057del; c.7192C>T; c.4389_4390del; c.6340C>T; c.5712_5713insT; c.3582del; c.1763C>A; c.7363del; c.6409_6410del; c.6817_6833del; c.2828_2829del; c.1711_1723del; c.4964_4965del; c.3019C>T; c.4558del; c.2395A>T; c.7083del; c.1785_1786delinsTT; c.2130del; c.3198_3199del; c.5274_5275insC; c.3221_3222del; c.1940_1941delinsT; c.6701del; c.7834G>T.

\n", "

Use the entry in the \"Key\" column to investigate whether specific variants display genotype-phenotype correlations

" ], "text/plain": [ @@ -660,414 +663,405 @@ " \n", " Intellectual disability [HP:0001249]\n", " 60\n", - " 25.210084\n", + " 25.104603\n", " 99\n", - " 41.596639\n", - " 0.000305\n", - " 0.008746\n", + " 41.422594\n", + " 0.000298\n", + " 0.008428\n", " \n", " \n", " Abnormality of mental function [HP:0011446]\n", " 66\n", - " 27.500000\n", + " 27.385892\n", " 113\n", - " 47.083333\n", - " 0.000380\n", - " 0.008746\n", + " 46.887967\n", + " 0.000375\n", + " 0.008428\n", " \n", " \n", " Neurodevelopmental abnormality [HP:0012759]\n", " 70\n", - " 28.925620\n", + " 28.806584\n", " 127\n", - " 52.479339\n", - " 0.001123\n", - " 0.017225\n", + " 52.263374\n", + " 0.000713\n", + " 0.010688\n", " \n", " \n", " Abnormality of the nervous system [HP:0000707]\n", " 73\n", - " 29.918033\n", + " 29.795918\n", " 135\n", - " 55.327869\n", - " 0.003385\n", - " 0.029320\n", + " 55.102041\n", + " 0.003406\n", + " 0.028437\n", " \n", " \n", " Abnormal nervous system physiology [HP:0012638]\n", " 73\n", - " 29.918033\n", + " 29.795918\n", " 135\n", - " 55.327869\n", - " 0.003385\n", - " 0.029320\n", + " 55.102041\n", + " 0.003406\n", + " 0.028437\n", " \n", " \n", - " Global developmental delay [HP:0001263]\n", + " Neurodevelopmental delay [HP:0012758]\n", " 47\n", - " 23.039216\n", + " 22.926829\n", " 86\n", - " 42.156863\n", - " 0.005883\n", - " 0.029320\n", + " 41.951220\n", + " 0.005774\n", + " 0.028437\n", " \n", " \n", - " Neurodevelopmental delay [HP:0012758]\n", + " Global developmental delay [HP:0001263]\n", " 47\n", - " 23.039216\n", + " 22.926829\n", " 86\n", - " 42.156863\n", - " 0.005883\n", - " 0.029320\n", + " 41.951220\n", + " 0.005774\n", + " 0.028437\n", " \n", " \n", - " Abnormal external nose morphology [HP:0010938]\n", + " Abnormal nasal morphology [HP:0005105]\n", " 42\n", - " 19.811321\n", + " 19.718310\n", " 70\n", - " 33.018868\n", - " 0.006374\n", - " 0.029320\n", + " 32.863850\n", + " 0.006319\n", + " 0.028437\n", " \n", " \n", - " Abnormal nasal morphology [HP:0005105]\n", + " Abnormality of the nose [HP:0000366]\n", " 42\n", - " 19.811321\n", + " 19.718310\n", " 70\n", - " 33.018868\n", - " 0.006374\n", - " 0.029320\n", + " 32.863850\n", + " 0.006319\n", + " 0.028437\n", " \n", " \n", - " Abnormality of the nose [HP:0000366]\n", + " Abnormal external nose morphology [HP:0010938]\n", " 42\n", - " 19.811321\n", + " 19.718310\n", " 70\n", - " 33.018868\n", - " 0.006374\n", - " 0.029320\n", + " 32.863850\n", + " 0.006319\n", + " 0.028437\n", " \n", " \n", " Abnormality of limbs [HP:0040064]\n", " 56\n", - " 23.236515\n", + " 23.140496\n", " 100\n", - " 41.493776\n", - " 0.059191\n", - " 0.197563\n", + " 41.322314\n", + " 0.044288\n", + " 0.151111\n", " \n", " \n", " Abnormality of the upper limb [HP:0002817]\n", " 56\n", - " 23.236515\n", + " 23.140496\n", " 100\n", - " 41.493776\n", - " 0.059191\n", - " 0.197563\n", + " 41.322314\n", + " 0.044288\n", + " 0.151111\n", " \n", " \n", " Abnormality of the hand [HP:0001155]\n", " 56\n", - " 23.236515\n", + " 23.140496\n", " 100\n", - " 41.493776\n", - " 0.059191\n", - " 0.197563\n", - " \n", - " \n", - " Abnormal lip morphology [HP:0000159]\n", - " 37\n", - " 17.129630\n", - " 66\n", - " 30.555556\n", - " 0.073012\n", - " 0.197563\n", + " 41.322314\n", + " 0.044288\n", + " 0.151111\n", " \n", " \n", - " Long philtrum [HP:0000343]\n", + " Abnormality of the philtrum [HP:0000288]\n", " 37\n", - " 17.129630\n", + " 17.050691\n", " 66\n", - " 30.555556\n", - " 0.073012\n", - " 0.197563\n", + " 30.414747\n", + " 0.053728\n", + " 0.151111\n", " \n", " \n", - " Abnormality of the philtrum [HP:0000288]\n", + " Abnormal upper lip morphology [HP:0000177]\n", " 37\n", - " 17.129630\n", + " 17.050691\n", " 66\n", - " 30.555556\n", - " 0.073012\n", - " 0.197563\n", + " 30.414747\n", + " 0.053728\n", + " 0.151111\n", " \n", " \n", - " Abnormal upper lip morphology [HP:0000177]\n", + " Abnormal lip morphology [HP:0000159]\n", " 37\n", - " 17.129630\n", + " 17.050691\n", " 66\n", - " 30.555556\n", - " 0.073012\n", - " 0.197563\n", + " 30.414747\n", + " 0.053728\n", + " 0.151111\n", " \n", " \n", " Abnormal ear morphology [HP:0031703]\n", " 21\n", - " 10.714286\n", + " 10.659898\n", " 37\n", - " 18.877551\n", - " 0.165308\n", - " 0.331764\n", + " 18.781726\n", + " 0.123006\n", + " 0.325604\n", " \n", " \n", - " Abnormality of the orbital region [HP:0000315]\n", + " Abnormality of the ocular adnexa [HP:0032039]\n", " 36\n", - " 17.142857\n", - " 69\n", - " 32.857143\n", - " 0.173094\n", - " 0.331764\n", + " 17.061611\n", + " 70\n", + " 33.175355\n", + " 0.173944\n", + " 0.340324\n", " \n", " \n", - " Abnormality of the integument [HP:0001574]\n", + " Abnormal skin adnexa morphology [HP:0011138]\n", " 36\n", - " 17.142857\n", - " 69\n", - " 32.857143\n", - " 0.173094\n", - " 0.331764\n", + " 17.061611\n", + " 70\n", + " 33.175355\n", + " 0.173944\n", + " 0.340324\n", " \n", " \n", - " Abnormality of the ocular adnexa [HP:0032039]\n", + " Abnormality of the integument [HP:0001574]\n", " 36\n", - " 17.142857\n", - " 69\n", - " 32.857143\n", - " 0.173094\n", - " 0.331764\n", + " 17.061611\n", + " 70\n", + " 33.175355\n", + " 0.173944\n", + " 0.340324\n", " \n", " \n", " Abnormal ocular adnexa morphology [HP:0030669]\n", " 36\n", - " 17.142857\n", - " 69\n", - " 32.857143\n", - " 0.173094\n", - " 0.331764\n", + " 17.061611\n", + " 70\n", + " 33.175355\n", + " 0.173944\n", + " 0.340324\n", " \n", " \n", " Abnormal hair morphology [HP:0001595]\n", " 36\n", - " 17.142857\n", - " 69\n", - " 32.857143\n", - " 0.173094\n", - " 0.331764\n", + " 17.061611\n", + " 70\n", + " 33.175355\n", + " 0.173944\n", + " 0.340324\n", " \n", " \n", - " Abnormal skin adnexa morphology [HP:0011138]\n", + " Abnormality of the orbital region [HP:0000315]\n", " 36\n", - " 17.142857\n", - " 69\n", - " 32.857143\n", - " 0.173094\n", - " 0.331764\n", + " 17.061611\n", + " 70\n", + " 33.175355\n", + " 0.173944\n", + " 0.340324\n", " \n", " \n", " Atypical behavior [HP:0000708]\n", " 24\n", - " 12.631579\n", + " 12.565445\n", " 48\n", - " 25.263158\n", - " 0.243055\n", - " 0.415513\n", + " 25.130890\n", + " 0.186939\n", + " 0.350511\n", " \n", " \n", " Abnormal facial shape [HP:0001999]\n", " 23\n", - " 11.855670\n", + " 11.794872\n", " 45\n", - " 23.195876\n", - " 0.243888\n", - " 0.415513\n", + " 23.076923\n", + " 0.242796\n", + " 0.420223\n", " \n", " \n", " Triangular face [HP:0000325]\n", " 23\n", - " 11.855670\n", + " 11.794872\n", " 45\n", - " 23.195876\n", - " 0.243888\n", - " 0.415513\n", + " 23.076923\n", + " 0.242796\n", + " 0.420223\n", " \n", " \n", - " Short stature [HP:0004322]\n", + " Abnormality of body height [HP:0000002]\n", " 40\n", - " 17.467249\n", + " 17.391304\n", " 75\n", - " 32.751092\n", + " 32.608696\n", " 0.319588\n", - " 0.474228\n", + " 0.479382\n", " \n", " \n", - " Abnormality of body height [HP:0000002]\n", + " Short stature [HP:0004322]\n", " 40\n", - " 17.467249\n", + " 17.391304\n", " 75\n", - " 32.751092\n", + " 32.608696\n", " 0.319588\n", - " 0.474228\n", + " 0.479382\n", " \n", " \n", - " Growth delay [HP:0001510]\n", + " Growth abnormality [HP:0001507]\n", " 40\n", - " 17.467249\n", + " 17.391304\n", " 75\n", - " 32.751092\n", + " 32.608696\n", " 0.319588\n", - " 0.474228\n", + " 0.479382\n", " \n", " \n", - " Growth abnormality [HP:0001507]\n", + " Growth delay [HP:0001510]\n", " 40\n", - " 17.467249\n", + " 17.391304\n", " 75\n", - " 32.751092\n", + " 32.608696\n", " 0.319588\n", - " 0.474228\n", + " 0.479382\n", " \n", " \n", " Cognitive impairment [HP:0100543]\n", " 16\n", - " 8.556150\n", + " 8.510638\n", " 35\n", - " 18.716578\n", - " 0.464138\n", - " 0.667198\n", + " 18.617021\n", + " 0.462538\n", + " 0.671426\n", " \n", " \n", - " Phenotypic abnormality [HP:0000118]\n", + " All [HP:0000001]\n", " 80\n", - " 31.872510\n", - " 168\n", - " 66.932271\n", - " 0.553478\n", - " 0.748823\n", + " 31.746032\n", + " 169\n", + " 67.063492\n", + " 0.553603\n", + " 0.754913\n", " \n", " \n", - " All [HP:0000001]\n", + " Phenotypic abnormality [HP:0000118]\n", " 80\n", - " 31.872510\n", - " 168\n", - " 66.932271\n", - " 0.553478\n", - " 0.748823\n", + " 31.746032\n", + " 169\n", + " 67.063492\n", + " 0.553603\n", + " 0.754913\n", " \n", " \n", - " Abnormality of the ear [HP:0000598]\n", - " 34\n", - " 16.267943\n", - " 77\n", - " 36.842105\n", - " 0.763746\n", - " 0.932469\n", + " Abnormal oral morphology [HP:0031816]\n", + " 65\n", + " 26.970954\n", + " 140\n", + " 58.091286\n", + " 0.700414\n", + " 0.875518\n", " \n", " \n", - " Abnormality of head or neck [HP:0000152]\n", - " 70\n", - " 28.925620\n", - " 150\n", - " 61.983471\n", - " 0.811212\n", - " 0.932469\n", + " Abnormality of the mouth [HP:0000153]\n", + " 65\n", + " 26.970954\n", + " 140\n", + " 58.091286\n", + " 0.700414\n", + " 0.875518\n", + " \n", + " \n", + " Abnormal oral cavity morphology [HP:0000163]\n", + " 65\n", + " 26.970954\n", + " 140\n", + " 58.091286\n", + " 0.700414\n", + " 0.875518\n", " \n", " \n", " Abnormality of the face [HP:0000271]\n", " 70\n", - " 28.925620\n", - " 150\n", - " 61.983471\n", - " 0.811212\n", - " 0.932469\n", + " 28.806584\n", + " 151\n", + " 62.139918\n", + " 0.811361\n", + " 0.936185\n", " \n", " \n", " Abnormality of the head [HP:0000234]\n", " 70\n", - " 28.925620\n", - " 150\n", - " 61.983471\n", - " 0.811212\n", - " 0.932469\n", + " 28.806584\n", + " 151\n", + " 62.139918\n", + " 0.811361\n", + " 0.936185\n", " \n", " \n", - " Abnormality of the mouth [HP:0000153]\n", - " 65\n", - " 27.083333\n", - " 140\n", - " 58.333333\n", - " 0.844225\n", - " 0.932469\n", - " \n", - " \n", - " Abnormal oral morphology [HP:0031816]\n", - " 65\n", - " 27.083333\n", - " 140\n", - " 58.333333\n", - " 0.844225\n", - " 0.932469\n", + " Abnormality of head or neck [HP:0000152]\n", + " 70\n", + " 28.806584\n", + " 151\n", + " 62.139918\n", + " 0.811361\n", + " 0.936185\n", " \n", " \n", - " Abnormal oral cavity morphology [HP:0000163]\n", - " 65\n", - " 27.083333\n", - " 140\n", - " 58.333333\n", - " 0.844225\n", - " 0.932469\n", + " Hearing abnormality [HP:0000364]\n", + " 22\n", + " 11.055276\n", + " 53\n", + " 26.633166\n", + " 0.872802\n", + " 0.942440\n", " \n", " \n", " Abnormal ear physiology [HP:0031704]\n", " 22\n", - " 11.111111\n", - " 52\n", - " 26.262626\n", - " 0.871656\n", - " 0.932469\n", + " 11.055276\n", + " 53\n", + " 26.633166\n", + " 0.872802\n", + " 0.942440\n", " \n", " \n", - " Hearing abnormality [HP:0000364]\n", - " 22\n", - " 11.111111\n", - " 52\n", - " 26.262626\n", - " 0.871656\n", - " 0.932469\n", + " Abnormality of the ear [HP:0000598]\n", + " 34\n", + " 16.190476\n", + " 78\n", + " 37.142857\n", + " 0.879611\n", + " 0.942440\n", " \n", " \n", " Abnormal dental morphology [HP:0006482]\n", " 58\n", - " 24.576271\n", + " 24.472574\n", " 124\n", - " 52.542373\n", + " 52.320675\n", " 1.000000\n", " 1.000000\n", " \n", " \n", " Abnormality of the dentition [HP:0000164]\n", " 58\n", - " 24.576271\n", + " 24.472574\n", " 124\n", - " 52.542373\n", + " 52.320675\n", " 1.000000\n", " 1.000000\n", " \n", " \n", " Macrodontia [HP:0001572]\n", " 58\n", - " 24.576271\n", + " 24.472574\n", " 124\n", - " 52.542373\n", + " 52.320675\n", " 1.000000\n", " 1.000000\n", " \n", @@ -1078,147 +1072,144 @@ "text/plain": [ "FRAMESHIFT_VARIANT on NM_013275.6 No Yes \\\n", " Count Percent Count \n", - "Intellectual disability [HP:0001249] 60 25.210084 99 \n", - "Abnormality of mental function [HP:0011446] 66 27.500000 113 \n", - "Neurodevelopmental abnormality [HP:0012759] 70 28.925620 127 \n", - "Abnormality of the nervous system [HP:0000707] 73 29.918033 135 \n", - "Abnormal nervous system physiology [HP:0012638] 73 29.918033 135 \n", - "Global developmental delay [HP:0001263] 47 23.039216 86 \n", - "Neurodevelopmental delay [HP:0012758] 47 23.039216 86 \n", - "Abnormal external nose morphology [HP:0010938] 42 19.811321 70 \n", - "Abnormal nasal morphology [HP:0005105] 42 19.811321 70 \n", - "Abnormality of the nose [HP:0000366] 42 19.811321 70 \n", - "Abnormality of limbs [HP:0040064] 56 23.236515 100 \n", - "Abnormality of the upper limb [HP:0002817] 56 23.236515 100 \n", - "Abnormality of the hand [HP:0001155] 56 23.236515 100 \n", - "Abnormal lip morphology [HP:0000159] 37 17.129630 66 \n", - "Long philtrum [HP:0000343] 37 17.129630 66 \n", - "Abnormality of the philtrum [HP:0000288] 37 17.129630 66 \n", - "Abnormal upper lip morphology [HP:0000177] 37 17.129630 66 \n", - "Abnormal ear morphology [HP:0031703] 21 10.714286 37 \n", - "Abnormality of the orbital region [HP:0000315] 36 17.142857 69 \n", - "Abnormality of the integument [HP:0001574] 36 17.142857 69 \n", - "Abnormality of the ocular adnexa [HP:0032039] 36 17.142857 69 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 36 17.142857 69 \n", - "Abnormal hair morphology [HP:0001595] 36 17.142857 69 \n", - "Abnormal skin adnexa morphology [HP:0011138] 36 17.142857 69 \n", - "Atypical behavior [HP:0000708] 24 12.631579 48 \n", - "Abnormal facial shape [HP:0001999] 23 11.855670 45 \n", - "Triangular face [HP:0000325] 23 11.855670 45 \n", - "Short stature [HP:0004322] 40 17.467249 75 \n", - "Abnormality of body height [HP:0000002] 40 17.467249 75 \n", - "Growth delay [HP:0001510] 40 17.467249 75 \n", - "Growth abnormality [HP:0001507] 40 17.467249 75 \n", - "Cognitive impairment [HP:0100543] 16 8.556150 35 \n", - "Phenotypic abnormality [HP:0000118] 80 31.872510 168 \n", - "All [HP:0000001] 80 31.872510 168 \n", - "Abnormality of the ear [HP:0000598] 34 16.267943 77 \n", - "Abnormality of head or neck [HP:0000152] 70 28.925620 150 \n", - "Abnormality of the face [HP:0000271] 70 28.925620 150 \n", - "Abnormality of the head [HP:0000234] 70 28.925620 150 \n", - "Abnormality of the mouth [HP:0000153] 65 27.083333 140 \n", - "Abnormal oral morphology [HP:0031816] 65 27.083333 140 \n", - "Abnormal oral cavity morphology [HP:0000163] 65 27.083333 140 \n", - "Abnormal ear physiology [HP:0031704] 22 11.111111 52 \n", - "Hearing abnormality [HP:0000364] 22 11.111111 52 \n", - "Abnormal dental morphology [HP:0006482] 58 24.576271 124 \n", - "Abnormality of the dentition [HP:0000164] 58 24.576271 124 \n", - "Macrodontia [HP:0001572] 58 24.576271 124 \n", + "Intellectual disability [HP:0001249] 60 25.104603 99 \n", + "Abnormality of mental function [HP:0011446] 66 27.385892 113 \n", + "Neurodevelopmental abnormality [HP:0012759] 70 28.806584 127 \n", + "Abnormality of the nervous system [HP:0000707] 73 29.795918 135 \n", + "Abnormal nervous system physiology [HP:0012638] 73 29.795918 135 \n", + "Neurodevelopmental delay [HP:0012758] 47 22.926829 86 \n", + "Global developmental delay [HP:0001263] 47 22.926829 86 \n", + "Abnormal nasal morphology [HP:0005105] 42 19.718310 70 \n", + "Abnormality of the nose [HP:0000366] 42 19.718310 70 \n", + "Abnormal external nose morphology [HP:0010938] 42 19.718310 70 \n", + "Abnormality of limbs [HP:0040064] 56 23.140496 100 \n", + "Abnormality of the upper limb [HP:0002817] 56 23.140496 100 \n", + "Abnormality of the hand [HP:0001155] 56 23.140496 100 \n", + "Abnormality of the philtrum [HP:0000288] 37 17.050691 66 \n", + "Abnormal upper lip morphology [HP:0000177] 37 17.050691 66 \n", + "Abnormal lip morphology [HP:0000159] 37 17.050691 66 \n", + "Abnormal ear morphology [HP:0031703] 21 10.659898 37 \n", + "Abnormality of the ocular adnexa [HP:0032039] 36 17.061611 70 \n", + "Abnormal skin adnexa morphology [HP:0011138] 36 17.061611 70 \n", + "Abnormality of the integument [HP:0001574] 36 17.061611 70 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 36 17.061611 70 \n", + "Abnormal hair morphology [HP:0001595] 36 17.061611 70 \n", + "Abnormality of the orbital region [HP:0000315] 36 17.061611 70 \n", + "Atypical behavior [HP:0000708] 24 12.565445 48 \n", + "Abnormal facial shape [HP:0001999] 23 11.794872 45 \n", + "Triangular face [HP:0000325] 23 11.794872 45 \n", + "Abnormality of body height [HP:0000002] 40 17.391304 75 \n", + "Short stature [HP:0004322] 40 17.391304 75 \n", + "Growth abnormality [HP:0001507] 40 17.391304 75 \n", + "Growth delay [HP:0001510] 40 17.391304 75 \n", + "Cognitive impairment [HP:0100543] 16 8.510638 35 \n", + "All [HP:0000001] 80 31.746032 169 \n", + "Phenotypic abnormality [HP:0000118] 80 31.746032 169 \n", + "Abnormal oral morphology [HP:0031816] 65 26.970954 140 \n", + "Abnormality of the mouth [HP:0000153] 65 26.970954 140 \n", + "Abnormal oral cavity morphology [HP:0000163] 65 26.970954 140 \n", + "Abnormality of the face [HP:0000271] 70 28.806584 151 \n", + "Abnormality of the head [HP:0000234] 70 28.806584 151 \n", + "Abnormality of head or neck [HP:0000152] 70 28.806584 151 \n", + "Hearing abnormality [HP:0000364] 22 11.055276 53 \n", + "Abnormal ear physiology [HP:0031704] 22 11.055276 53 \n", + "Abnormality of the ear [HP:0000598] 34 16.190476 78 \n", + "Abnormal dental morphology [HP:0006482] 58 24.472574 124 \n", + "Abnormality of the dentition [HP:0000164] 58 24.472574 124 \n", + "Macrodontia [HP:0001572] 58 24.472574 124 \n", "\n", "FRAMESHIFT_VARIANT on NM_013275.6 \\\n", " Percent p value \n", - "Intellectual disability [HP:0001249] 41.596639 0.000305 \n", - "Abnormality of mental function [HP:0011446] 47.083333 0.000380 \n", - "Neurodevelopmental abnormality [HP:0012759] 52.479339 0.001123 \n", - "Abnormality of the nervous system [HP:0000707] 55.327869 0.003385 \n", - "Abnormal nervous system physiology [HP:0012638] 55.327869 0.003385 \n", - "Global developmental delay [HP:0001263] 42.156863 0.005883 \n", - "Neurodevelopmental delay [HP:0012758] 42.156863 0.005883 \n", - "Abnormal external nose morphology [HP:0010938] 33.018868 0.006374 \n", - "Abnormal nasal morphology [HP:0005105] 33.018868 0.006374 \n", - "Abnormality of the nose [HP:0000366] 33.018868 0.006374 \n", - "Abnormality of limbs [HP:0040064] 41.493776 0.059191 \n", - "Abnormality of the upper limb [HP:0002817] 41.493776 0.059191 \n", - "Abnormality of the hand [HP:0001155] 41.493776 0.059191 \n", - "Abnormal lip morphology [HP:0000159] 30.555556 0.073012 \n", - "Long philtrum [HP:0000343] 30.555556 0.073012 \n", - "Abnormality of the philtrum [HP:0000288] 30.555556 0.073012 \n", - "Abnormal upper lip morphology [HP:0000177] 30.555556 0.073012 \n", - "Abnormal ear morphology [HP:0031703] 18.877551 0.165308 \n", - "Abnormality of the orbital region [HP:0000315] 32.857143 0.173094 \n", - "Abnormality of the integument [HP:0001574] 32.857143 0.173094 \n", - "Abnormality of the ocular adnexa [HP:0032039] 32.857143 0.173094 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 32.857143 0.173094 \n", - "Abnormal hair morphology [HP:0001595] 32.857143 0.173094 \n", - "Abnormal skin adnexa morphology [HP:0011138] 32.857143 0.173094 \n", - "Atypical behavior [HP:0000708] 25.263158 0.243055 \n", - "Abnormal facial shape [HP:0001999] 23.195876 0.243888 \n", - "Triangular face [HP:0000325] 23.195876 0.243888 \n", - "Short stature [HP:0004322] 32.751092 0.319588 \n", - "Abnormality of body height [HP:0000002] 32.751092 0.319588 \n", - "Growth delay [HP:0001510] 32.751092 0.319588 \n", - "Growth abnormality [HP:0001507] 32.751092 0.319588 \n", - "Cognitive impairment [HP:0100543] 18.716578 0.464138 \n", - "Phenotypic abnormality [HP:0000118] 66.932271 0.553478 \n", - "All [HP:0000001] 66.932271 0.553478 \n", - "Abnormality of the ear [HP:0000598] 36.842105 0.763746 \n", - "Abnormality of head or neck [HP:0000152] 61.983471 0.811212 \n", - "Abnormality of the face [HP:0000271] 61.983471 0.811212 \n", - "Abnormality of the head [HP:0000234] 61.983471 0.811212 \n", - "Abnormality of the mouth [HP:0000153] 58.333333 0.844225 \n", - "Abnormal oral morphology [HP:0031816] 58.333333 0.844225 \n", - "Abnormal oral cavity morphology [HP:0000163] 58.333333 0.844225 \n", - "Abnormal ear physiology [HP:0031704] 26.262626 0.871656 \n", - "Hearing abnormality [HP:0000364] 26.262626 0.871656 \n", - "Abnormal dental morphology [HP:0006482] 52.542373 1.000000 \n", - "Abnormality of the dentition [HP:0000164] 52.542373 1.000000 \n", - "Macrodontia [HP:0001572] 52.542373 1.000000 \n", + "Intellectual disability [HP:0001249] 41.422594 0.000298 \n", + "Abnormality of mental function [HP:0011446] 46.887967 0.000375 \n", + "Neurodevelopmental abnormality [HP:0012759] 52.263374 0.000713 \n", + "Abnormality of the nervous system [HP:0000707] 55.102041 0.003406 \n", + "Abnormal nervous system physiology [HP:0012638] 55.102041 0.003406 \n", + "Neurodevelopmental delay [HP:0012758] 41.951220 0.005774 \n", + "Global developmental delay [HP:0001263] 41.951220 0.005774 \n", + "Abnormal nasal morphology [HP:0005105] 32.863850 0.006319 \n", + "Abnormality of the nose [HP:0000366] 32.863850 0.006319 \n", + "Abnormal external nose morphology [HP:0010938] 32.863850 0.006319 \n", + "Abnormality of limbs [HP:0040064] 41.322314 0.044288 \n", + "Abnormality of the upper limb [HP:0002817] 41.322314 0.044288 \n", + "Abnormality of the hand [HP:0001155] 41.322314 0.044288 \n", + "Abnormality of the philtrum [HP:0000288] 30.414747 0.053728 \n", + "Abnormal upper lip morphology [HP:0000177] 30.414747 0.053728 \n", + "Abnormal lip morphology [HP:0000159] 30.414747 0.053728 \n", + "Abnormal ear morphology [HP:0031703] 18.781726 0.123006 \n", + "Abnormality of the ocular adnexa [HP:0032039] 33.175355 0.173944 \n", + "Abnormal skin adnexa morphology [HP:0011138] 33.175355 0.173944 \n", + "Abnormality of the integument [HP:0001574] 33.175355 0.173944 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 33.175355 0.173944 \n", + "Abnormal hair morphology [HP:0001595] 33.175355 0.173944 \n", + "Abnormality of the orbital region [HP:0000315] 33.175355 0.173944 \n", + "Atypical behavior [HP:0000708] 25.130890 0.186939 \n", + "Abnormal facial shape [HP:0001999] 23.076923 0.242796 \n", + "Triangular face [HP:0000325] 23.076923 0.242796 \n", + "Abnormality of body height [HP:0000002] 32.608696 0.319588 \n", + "Short stature [HP:0004322] 32.608696 0.319588 \n", + "Growth abnormality [HP:0001507] 32.608696 0.319588 \n", + "Growth delay [HP:0001510] 32.608696 0.319588 \n", + "Cognitive impairment [HP:0100543] 18.617021 0.462538 \n", + "All [HP:0000001] 67.063492 0.553603 \n", + "Phenotypic abnormality [HP:0000118] 67.063492 0.553603 \n", + "Abnormal oral morphology [HP:0031816] 58.091286 0.700414 \n", + "Abnormality of the mouth [HP:0000153] 58.091286 0.700414 \n", + "Abnormal oral cavity morphology [HP:0000163] 58.091286 0.700414 \n", + "Abnormality of the face [HP:0000271] 62.139918 0.811361 \n", + "Abnormality of the head [HP:0000234] 62.139918 0.811361 \n", + "Abnormality of head or neck [HP:0000152] 62.139918 0.811361 \n", + "Hearing abnormality [HP:0000364] 26.633166 0.872802 \n", + "Abnormal ear physiology [HP:0031704] 26.633166 0.872802 \n", + "Abnormality of the ear [HP:0000598] 37.142857 0.879611 \n", + "Abnormal dental morphology [HP:0006482] 52.320675 1.000000 \n", + "Abnormality of the dentition [HP:0000164] 52.320675 1.000000 \n", + "Macrodontia [HP:0001572] 52.320675 1.000000 \n", "\n", "FRAMESHIFT_VARIANT on NM_013275.6 \n", " Corrected p value \n", - "Intellectual disability [HP:0001249] 0.008746 \n", - "Abnormality of mental function [HP:0011446] 0.008746 \n", - "Neurodevelopmental abnormality [HP:0012759] 0.017225 \n", - "Abnormality of the nervous system [HP:0000707] 0.029320 \n", - "Abnormal nervous system physiology [HP:0012638] 0.029320 \n", - "Global developmental delay [HP:0001263] 0.029320 \n", - "Neurodevelopmental delay [HP:0012758] 0.029320 \n", - "Abnormal external nose morphology [HP:0010938] 0.029320 \n", - "Abnormal nasal morphology [HP:0005105] 0.029320 \n", - "Abnormality of the nose [HP:0000366] 0.029320 \n", - "Abnormality of limbs [HP:0040064] 0.197563 \n", - "Abnormality of the upper limb [HP:0002817] 0.197563 \n", - "Abnormality of the hand [HP:0001155] 0.197563 \n", - "Abnormal lip morphology [HP:0000159] 0.197563 \n", - "Long philtrum [HP:0000343] 0.197563 \n", - "Abnormality of the philtrum [HP:0000288] 0.197563 \n", - "Abnormal upper lip morphology [HP:0000177] 0.197563 \n", - "Abnormal ear morphology [HP:0031703] 0.331764 \n", - "Abnormality of the orbital region [HP:0000315] 0.331764 \n", - "Abnormality of the integument [HP:0001574] 0.331764 \n", - "Abnormality of the ocular adnexa [HP:0032039] 0.331764 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 0.331764 \n", - "Abnormal hair morphology [HP:0001595] 0.331764 \n", - "Abnormal skin adnexa morphology [HP:0011138] 0.331764 \n", - "Atypical behavior [HP:0000708] 0.415513 \n", - "Abnormal facial shape [HP:0001999] 0.415513 \n", - "Triangular face [HP:0000325] 0.415513 \n", - "Short stature [HP:0004322] 0.474228 \n", - "Abnormality of body height [HP:0000002] 0.474228 \n", - "Growth delay [HP:0001510] 0.474228 \n", - "Growth abnormality [HP:0001507] 0.474228 \n", - "Cognitive impairment [HP:0100543] 0.667198 \n", - "Phenotypic abnormality [HP:0000118] 0.748823 \n", - "All [HP:0000001] 0.748823 \n", - "Abnormality of the ear [HP:0000598] 0.932469 \n", - "Abnormality of head or neck [HP:0000152] 0.932469 \n", - "Abnormality of the face [HP:0000271] 0.932469 \n", - "Abnormality of the head [HP:0000234] 0.932469 \n", - "Abnormality of the mouth [HP:0000153] 0.932469 \n", - "Abnormal oral morphology [HP:0031816] 0.932469 \n", - "Abnormal oral cavity morphology [HP:0000163] 0.932469 \n", - "Abnormal ear physiology [HP:0031704] 0.932469 \n", - "Hearing abnormality [HP:0000364] 0.932469 \n", + "Intellectual disability [HP:0001249] 0.008428 \n", + "Abnormality of mental function [HP:0011446] 0.008428 \n", + "Neurodevelopmental abnormality [HP:0012759] 0.010688 \n", + "Abnormality of the nervous system [HP:0000707] 0.028437 \n", + "Abnormal nervous system physiology [HP:0012638] 0.028437 \n", + "Neurodevelopmental delay [HP:0012758] 0.028437 \n", + "Global developmental delay [HP:0001263] 0.028437 \n", + "Abnormal nasal morphology [HP:0005105] 0.028437 \n", + "Abnormality of the nose [HP:0000366] 0.028437 \n", + "Abnormal external nose morphology [HP:0010938] 0.028437 \n", + "Abnormality of limbs [HP:0040064] 0.151111 \n", + "Abnormality of the upper limb [HP:0002817] 0.151111 \n", + "Abnormality of the hand [HP:0001155] 0.151111 \n", + "Abnormality of the philtrum [HP:0000288] 0.151111 \n", + "Abnormal upper lip morphology [HP:0000177] 0.151111 \n", + "Abnormal lip morphology [HP:0000159] 0.151111 \n", + "Abnormal ear morphology [HP:0031703] 0.325604 \n", + "Abnormality of the ocular adnexa [HP:0032039] 0.340324 \n", + "Abnormal skin adnexa morphology [HP:0011138] 0.340324 \n", + "Abnormality of the integument [HP:0001574] 0.340324 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 0.340324 \n", + "Abnormal hair morphology [HP:0001595] 0.340324 \n", + "Abnormality of the orbital region [HP:0000315] 0.340324 \n", + "Atypical behavior [HP:0000708] 0.350511 \n", + "Abnormal facial shape [HP:0001999] 0.420223 \n", + "Triangular face [HP:0000325] 0.420223 \n", + "Abnormality of body height [HP:0000002] 0.479382 \n", + "Short stature [HP:0004322] 0.479382 \n", + "Growth abnormality [HP:0001507] 0.479382 \n", + "Growth delay [HP:0001510] 0.479382 \n", + "Cognitive impairment [HP:0100543] 0.671426 \n", + "All [HP:0000001] 0.754913 \n", + "Phenotypic abnormality [HP:0000118] 0.754913 \n", + "Abnormal oral morphology [HP:0031816] 0.875518 \n", + "Abnormality of the mouth [HP:0000153] 0.875518 \n", + "Abnormal oral cavity morphology [HP:0000163] 0.875518 \n", + "Abnormality of the face [HP:0000271] 0.936185 \n", + "Abnormality of the head [HP:0000234] 0.936185 \n", + "Abnormality of head or neck [HP:0000152] 0.936185 \n", + "Hearing abnormality [HP:0000364] 0.942440 \n", + "Abnormal ear physiology [HP:0031704] 0.942440 \n", + "Abnormality of the ear [HP:0000598] 0.942440 \n", "Abnormal dental morphology [HP:0006482] 1.000000 \n", "Abnormality of the dentition [HP:0000164] 1.000000 \n", "Macrodontia [HP:0001572] 1.000000 " @@ -1289,414 +1280,405 @@ " \n", " Neurodevelopmental abnormality [HP:0012759]\n", " 176\n", - " 72.727273\n", + " 72.427984\n", " 21\n", - " 8.677686\n", - " 0.007993\n", - " 0.169079\n", + " 8.641975\n", + " 0.014389\n", + " 0.174046\n", + " \n", + " \n", + " Intellectual disability [HP:0001249]\n", + " 144\n", + " 60.251046\n", + " 15\n", + " 6.276151\n", + " 0.015381\n", + " 0.174046\n", " \n", " \n", " Abnormal nervous system physiology [HP:0012638]\n", " 185\n", - " 75.819672\n", + " 75.510204\n", " 23\n", - " 9.426230\n", - " 0.014355\n", - " 0.169079\n", + " 9.387755\n", + " 0.016113\n", + " 0.174046\n", " \n", " \n", " Abnormality of the nervous system [HP:0000707]\n", " 185\n", - " 75.819672\n", + " 75.510204\n", " 23\n", - " 9.426230\n", - " 0.014355\n", - " 0.169079\n", - " \n", - " \n", - " Intellectual disability [HP:0001249]\n", - " 144\n", - " 60.504202\n", - " 15\n", - " 6.302521\n", - " 0.014702\n", - " 0.169079\n", + " 9.387755\n", + " 0.016113\n", + " 0.174046\n", " \n", " \n", " Phenotypic abnormality [HP:0000118]\n", - " 217\n", - " 86.454183\n", + " 218\n", + " 86.507937\n", " 31\n", - " 12.350598\n", - " 0.046296\n", - " 0.214567\n", + " 12.301587\n", + " 0.045945\n", + " 0.174046\n", " \n", " \n", " All [HP:0000001]\n", - " 217\n", - " 86.454183\n", + " 218\n", + " 86.507937\n", " 31\n", - " 12.350598\n", - " 0.046296\n", - " 0.214567\n", + " 12.301587\n", + " 0.045945\n", + " 0.174046\n", " \n", " \n", " Abnormality of mental function [HP:0011446]\n", " 160\n", - " 66.666667\n", + " 66.390041\n", " 19\n", - " 7.916667\n", - " 0.048016\n", - " 0.214567\n", - " \n", - " \n", - " Neurodevelopmental delay [HP:0012758]\n", - " 119\n", - " 58.333333\n", - " 14\n", - " 6.862745\n", - " 0.056706\n", - " 0.214567\n", - " \n", - " \n", - " Global developmental delay [HP:0001263]\n", - " 119\n", - " 58.333333\n", - " 14\n", - " 6.862745\n", - " 0.056706\n", - " 0.214567\n", + " 7.883817\n", + " 0.050034\n", + " 0.174046\n", " \n", " \n", - " Abnormality of the ear [HP:0000598]\n", - " 101\n", - " 48.325359\n", + " Abnormality of the orbital region [HP:0000315]\n", + " 96\n", + " 45.497630\n", " 10\n", - " 4.784689\n", - " 0.066000\n", - " 0.214567\n", + " 4.739336\n", + " 0.050625\n", + " 0.174046\n", " \n", " \n", - " Abnormality of the ocular adnexa [HP:0032039]\n", - " 95\n", - " 45.238095\n", + " Abnormal ocular adnexa morphology [HP:0030669]\n", + " 96\n", + " 45.497630\n", " 10\n", - " 4.761905\n", - " 0.074632\n", - " 0.214567\n", + " 4.739336\n", + " 0.050625\n", + " 0.174046\n", " \n", " \n", - " Abnormality of the orbital region [HP:0000315]\n", - " 95\n", - " 45.238095\n", + " Abnormal hair morphology [HP:0001595]\n", + " 96\n", + " 45.497630\n", " 10\n", - " 4.761905\n", - " 0.074632\n", - " 0.214567\n", + " 4.739336\n", + " 0.050625\n", + " 0.174046\n", " \n", " \n", " Abnormality of the integument [HP:0001574]\n", - " 95\n", - " 45.238095\n", + " 96\n", + " 45.497630\n", " 10\n", - " 4.761905\n", - " 0.074632\n", - " 0.214567\n", + " 4.739336\n", + " 0.050625\n", + " 0.174046\n", " \n", " \n", " Abnormal skin adnexa morphology [HP:0011138]\n", - " 95\n", - " 45.238095\n", + " 96\n", + " 45.497630\n", " 10\n", - " 4.761905\n", - " 0.074632\n", - " 0.214567\n", + " 4.739336\n", + " 0.050625\n", + " 0.174046\n", " \n", " \n", - " Abnormal hair morphology [HP:0001595]\n", - " 95\n", - " 45.238095\n", + " Abnormality of the ocular adnexa [HP:0032039]\n", + " 96\n", + " 45.497630\n", " 10\n", - " 4.761905\n", - " 0.074632\n", - " 0.214567\n", + " 4.739336\n", + " 0.050625\n", + " 0.174046\n", " \n", " \n", - " Abnormal ocular adnexa morphology [HP:0030669]\n", - " 95\n", - " 45.238095\n", + " Global developmental delay [HP:0001263]\n", + " 119\n", + " 58.048780\n", + " 14\n", + " 6.829268\n", + " 0.058015\n", + " 0.174046\n", + " \n", + " \n", + " Neurodevelopmental delay [HP:0012758]\n", + " 119\n", + " 58.048780\n", + " 14\n", + " 6.829268\n", + " 0.058015\n", + " 0.174046\n", + " \n", + " \n", + " Abnormality of the ear [HP:0000598]\n", + " 102\n", + " 48.571429\n", " 10\n", " 4.761905\n", - " 0.074632\n", - " 0.214567\n", + " 0.065729\n", + " 0.184863\n", " \n", " \n", - " Abnormality of the face [HP:0000271]\n", - " 193\n", - " 79.752066\n", + " Abnormality of head or neck [HP:0000152]\n", + " 194\n", + " 79.835391\n", " 27\n", - " 11.157025\n", - " 0.093495\n", - " 0.226357\n", + " 11.111111\n", + " 0.092993\n", + " 0.220246\n", " \n", " \n", " Abnormality of the head [HP:0000234]\n", - " 193\n", - " 79.752066\n", + " 194\n", + " 79.835391\n", " 27\n", - " 11.157025\n", - " 0.093495\n", - " 0.226357\n", + " 11.111111\n", + " 0.092993\n", + " 0.220246\n", " \n", " \n", - " Abnormality of head or neck [HP:0000152]\n", - " 193\n", - " 79.752066\n", + " Abnormality of the face [HP:0000271]\n", + " 194\n", + " 79.835391\n", " 27\n", - " 11.157025\n", - " 0.093495\n", - " 0.226357\n", + " 11.111111\n", + " 0.092993\n", + " 0.220246\n", " \n", " \n", - " Abnormal oral morphology [HP:0031816]\n", + " Abnormality of the mouth [HP:0000153]\n", " 180\n", - " 75.000000\n", + " 74.688797\n", " 25\n", - " 10.416667\n", - " 0.109604\n", - " 0.229172\n", + " 10.373444\n", + " 0.117228\n", + " 0.239785\n", " \n", " \n", - " Abnormality of the mouth [HP:0000153]\n", + " Abnormal oral cavity morphology [HP:0000163]\n", " 180\n", - " 75.000000\n", + " 74.688797\n", " 25\n", - " 10.416667\n", - " 0.109604\n", - " 0.229172\n", + " 10.373444\n", + " 0.117228\n", + " 0.239785\n", " \n", " \n", - " Abnormal oral cavity morphology [HP:0000163]\n", + " Abnormal oral morphology [HP:0031816]\n", " 180\n", - " 75.000000\n", + " 74.688797\n", " 25\n", - " 10.416667\n", - " 0.109604\n", - " 0.229172\n", + " 10.373444\n", + " 0.117228\n", + " 0.239785\n", " \n", " \n", " Abnormal facial shape [HP:0001999]\n", " 62\n", - " 31.958763\n", + " 31.794872\n", " 6\n", - " 3.092784\n", - " 0.134129\n", - " 0.257080\n", + " 3.076923\n", + " 0.134696\n", + " 0.252556\n", " \n", " \n", " Triangular face [HP:0000325]\n", " 62\n", - " 31.958763\n", + " 31.794872\n", " 6\n", - " 3.092784\n", - " 0.134129\n", - " 0.257080\n", + " 3.076923\n", + " 0.134696\n", + " 0.252556\n", " \n", " \n", - " Hearing abnormality [HP:0000364]\n", - " 67\n", - " 33.838384\n", + " Abnormal ear physiology [HP:0031704]\n", + " 68\n", + " 34.170854\n", " 7\n", - " 3.535354\n", - " 0.205373\n", - " 0.338570\n", + " 3.517588\n", + " 0.147568\n", + " 0.255407\n", " \n", " \n", - " Abnormal ear physiology [HP:0031704]\n", - " 67\n", - " 33.838384\n", + " Hearing abnormality [HP:0000364]\n", + " 68\n", + " 34.170854\n", " 7\n", - " 3.535354\n", - " 0.205373\n", - " 0.338570\n", + " 3.517588\n", + " 0.147568\n", + " 0.255407\n", " \n", " \n", - " Abnormal upper lip morphology [HP:0000177]\n", + " Abnormal lip morphology [HP:0000159]\n", " 92\n", - " 42.592593\n", + " 42.396313\n", " 11\n", - " 5.092593\n", - " 0.238468\n", - " 0.338570\n", + " 5.069124\n", + " 0.239690\n", + " 0.343181\n", " \n", " \n", " Abnormality of the philtrum [HP:0000288]\n", " 92\n", - " 42.592593\n", - " 11\n", - " 5.092593\n", - " 0.238468\n", - " 0.338570\n", - " \n", - " \n", - " Long philtrum [HP:0000343]\n", - " 92\n", - " 42.592593\n", + " 42.396313\n", " 11\n", - " 5.092593\n", - " 0.238468\n", - " 0.338570\n", + " 5.069124\n", + " 0.239690\n", + " 0.343181\n", " \n", " \n", - " Abnormal lip morphology [HP:0000159]\n", + " Abnormal upper lip morphology [HP:0000177]\n", " 92\n", - " 42.592593\n", + " 42.396313\n", " 11\n", - " 5.092593\n", - " 0.238468\n", - " 0.338570\n", + " 5.069124\n", + " 0.239690\n", + " 0.343181\n", " \n", " \n", - " Abnormality of the nose [HP:0000366]\n", + " Abnormal nasal morphology [HP:0005105]\n", " 99\n", - " 46.698113\n", + " 46.478873\n", " 13\n", - " 6.132075\n", - " 0.242887\n", - " 0.338570\n", + " 6.103286\n", + " 0.244040\n", + " 0.343181\n", " \n", " \n", - " Abnormal nasal morphology [HP:0005105]\n", + " Abnormality of the nose [HP:0000366]\n", " 99\n", - " 46.698113\n", + " 46.478873\n", " 13\n", - " 6.132075\n", - " 0.242887\n", - " 0.338570\n", + " 6.103286\n", + " 0.244040\n", + " 0.343181\n", " \n", " \n", " Abnormal external nose morphology [HP:0010938]\n", " 99\n", - " 46.698113\n", + " 46.478873\n", " 13\n", - " 6.132075\n", - " 0.242887\n", - " 0.338570\n", + " 6.103286\n", + " 0.244040\n", + " 0.343181\n", " \n", " \n", " Abnormal ear morphology [HP:0031703]\n", " 52\n", - " 26.530612\n", + " 26.395939\n", " 6\n", - " 3.061224\n", - " 0.375674\n", - " 0.508265\n", + " 3.045685\n", + " 0.376567\n", + " 0.513501\n", " \n", " \n", " Atypical behavior [HP:0000708]\n", " 64\n", - " 33.684211\n", + " 33.507853\n", " 8\n", - " 4.210526\n", - " 0.396639\n", - " 0.521297\n", + " 4.188482\n", + " 0.398051\n", + " 0.526832\n", " \n", " \n", - " Growth delay [HP:0001510]\n", + " Short stature [HP:0004322]\n", " 101\n", - " 44.104803\n", + " 43.913043\n", " 14\n", - " 6.113537\n", - " 0.452237\n", - " 0.533408\n", + " 6.086957\n", + " 0.568154\n", + " 0.672813\n", " \n", " \n", - " Abnormality of body height [HP:0000002]\n", + " Growth abnormality [HP:0001507]\n", " 101\n", - " 44.104803\n", + " 43.913043\n", " 14\n", - " 6.113537\n", - " 0.452237\n", - " 0.533408\n", + " 6.086957\n", + " 0.568154\n", + " 0.672813\n", " \n", " \n", - " Short stature [HP:0004322]\n", + " Abnormality of body height [HP:0000002]\n", " 101\n", - " 44.104803\n", + " 43.913043\n", " 14\n", - " 6.113537\n", - " 0.452237\n", - " 0.533408\n", + " 6.086957\n", + " 0.568154\n", + " 0.672813\n", " \n", " \n", - " Growth abnormality [HP:0001507]\n", + " Growth delay [HP:0001510]\n", " 101\n", - " 44.104803\n", + " 43.913043\n", " 14\n", - " 6.113537\n", - " 0.452237\n", - " 0.533408\n", + " 6.086957\n", + " 0.568154\n", + " 0.672813\n", " \n", " \n", " Abnormality of the dentition [HP:0000164]\n", " 159\n", - " 67.372881\n", + " 67.088608\n", " 23\n", - " 9.745763\n", - " 0.651760\n", - " 0.713833\n", + " 9.704641\n", + " 0.819515\n", + " 0.865969\n", " \n", " \n", " Abnormal dental morphology [HP:0006482]\n", " 159\n", - " 67.372881\n", + " 67.088608\n", " 23\n", - " 9.745763\n", - " 0.651760\n", - " 0.713833\n", + " 9.704641\n", + " 0.819515\n", + " 0.865969\n", " \n", " \n", " Macrodontia [HP:0001572]\n", " 159\n", - " 67.372881\n", + " 67.088608\n", " 23\n", - " 9.745763\n", - " 0.651760\n", - " 0.713833\n", + " 9.704641\n", + " 0.819515\n", + " 0.865969\n", " \n", " \n", - " Abnormality of limbs [HP:0040064]\n", + " Abnormality of the hand [HP:0001155]\n", " 134\n", - " 55.601660\n", + " 55.371901\n", " 22\n", - " 9.128631\n", - " 0.847288\n", - " 0.866116\n", + " 9.090909\n", + " 0.846725\n", + " 0.865969\n", " \n", " \n", " Abnormality of the upper limb [HP:0002817]\n", " 134\n", - " 55.601660\n", + " 55.371901\n", " 22\n", - " 9.128631\n", - " 0.847288\n", - " 0.866116\n", + " 9.090909\n", + " 0.846725\n", + " 0.865969\n", " \n", " \n", - " Abnormality of the hand [HP:0001155]\n", + " Abnormality of limbs [HP:0040064]\n", " 134\n", - " 55.601660\n", + " 55.371901\n", " 22\n", - " 9.128631\n", - " 0.847288\n", - " 0.866116\n", + " 9.090909\n", + " 0.846725\n", + " 0.865969\n", " \n", " \n", " Cognitive impairment [HP:0100543]\n", " 44\n", - " 23.529412\n", + " 23.404255\n", " 7\n", - " 3.743316\n", + " 3.723404\n", " 1.000000\n", " 1.000000\n", " \n", @@ -1707,198 +1689,194 @@ "text/plain": [ ">=1 allele of the variant 16_89284634_89284639_GTGTTT_G No \\\n", " Count Percent \n", - "Neurodevelopmental abnormality [HP:0012759] 176 72.727273 \n", - "Abnormal nervous system physiology [HP:0012638] 185 75.819672 \n", - "Abnormality of the nervous system [HP:0000707] 185 75.819672 \n", - "Intellectual disability [HP:0001249] 144 60.504202 \n", - "Phenotypic abnormality [HP:0000118] 217 86.454183 \n", - "All [HP:0000001] 217 86.454183 \n", - "Abnormality of mental function [HP:0011446] 160 66.666667 \n", - "Neurodevelopmental delay [HP:0012758] 119 58.333333 \n", - "Global developmental delay [HP:0001263] 119 58.333333 \n", - "Abnormality of the ear [HP:0000598] 101 48.325359 \n", - "Abnormality of the ocular adnexa [HP:0032039] 95 45.238095 \n", - "Abnormality of the orbital region [HP:0000315] 95 45.238095 \n", - "Abnormality of the integument [HP:0001574] 95 45.238095 \n", - "Abnormal skin adnexa morphology [HP:0011138] 95 45.238095 \n", - "Abnormal hair morphology [HP:0001595] 95 45.238095 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 95 45.238095 \n", - "Abnormality of the face [HP:0000271] 193 79.752066 \n", - "Abnormality of the head [HP:0000234] 193 79.752066 \n", - "Abnormality of head or neck [HP:0000152] 193 79.752066 \n", - "Abnormal oral morphology [HP:0031816] 180 75.000000 \n", - "Abnormality of the mouth [HP:0000153] 180 75.000000 \n", - "Abnormal oral cavity morphology [HP:0000163] 180 75.000000 \n", - "Abnormal facial shape [HP:0001999] 62 31.958763 \n", - "Triangular face [HP:0000325] 62 31.958763 \n", - "Hearing abnormality [HP:0000364] 67 33.838384 \n", - "Abnormal ear physiology [HP:0031704] 67 33.838384 \n", - "Abnormal upper lip morphology [HP:0000177] 92 42.592593 \n", - "Abnormality of the philtrum [HP:0000288] 92 42.592593 \n", - "Long philtrum [HP:0000343] 92 42.592593 \n", - "Abnormal lip morphology [HP:0000159] 92 42.592593 \n", - "Abnormality of the nose [HP:0000366] 99 46.698113 \n", - "Abnormal nasal morphology [HP:0005105] 99 46.698113 \n", - "Abnormal external nose morphology [HP:0010938] 99 46.698113 \n", - "Abnormal ear morphology [HP:0031703] 52 26.530612 \n", - "Atypical behavior [HP:0000708] 64 33.684211 \n", - "Growth delay [HP:0001510] 101 44.104803 \n", - "Abnormality of body height [HP:0000002] 101 44.104803 \n", - "Short stature [HP:0004322] 101 44.104803 \n", - "Growth abnormality [HP:0001507] 101 44.104803 \n", - "Abnormality of the dentition [HP:0000164] 159 67.372881 \n", - "Abnormal dental morphology [HP:0006482] 159 67.372881 \n", - "Macrodontia [HP:0001572] 159 67.372881 \n", - "Abnormality of limbs [HP:0040064] 134 55.601660 \n", - "Abnormality of the upper limb [HP:0002817] 134 55.601660 \n", - "Abnormality of the hand [HP:0001155] 134 55.601660 \n", - "Cognitive impairment [HP:0100543] 44 23.529412 \n", + "Neurodevelopmental abnormality [HP:0012759] 176 72.427984 \n", + "Intellectual disability [HP:0001249] 144 60.251046 \n", + "Abnormal nervous system physiology [HP:0012638] 185 75.510204 \n", + "Abnormality of the nervous system [HP:0000707] 185 75.510204 \n", + "Phenotypic abnormality [HP:0000118] 218 86.507937 \n", + "All [HP:0000001] 218 86.507937 \n", + "Abnormality of mental function [HP:0011446] 160 66.390041 \n", + "Abnormality of the orbital region [HP:0000315] 96 45.497630 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 96 45.497630 \n", + "Abnormal hair morphology [HP:0001595] 96 45.497630 \n", + "Abnormality of the integument [HP:0001574] 96 45.497630 \n", + "Abnormal skin adnexa morphology [HP:0011138] 96 45.497630 \n", + "Abnormality of the ocular adnexa [HP:0032039] 96 45.497630 \n", + "Global developmental delay [HP:0001263] 119 58.048780 \n", + "Neurodevelopmental delay [HP:0012758] 119 58.048780 \n", + "Abnormality of the ear [HP:0000598] 102 48.571429 \n", + "Abnormality of head or neck [HP:0000152] 194 79.835391 \n", + "Abnormality of the head [HP:0000234] 194 79.835391 \n", + "Abnormality of the face [HP:0000271] 194 79.835391 \n", + "Abnormality of the mouth [HP:0000153] 180 74.688797 \n", + "Abnormal oral cavity morphology [HP:0000163] 180 74.688797 \n", + "Abnormal oral morphology [HP:0031816] 180 74.688797 \n", + "Abnormal facial shape [HP:0001999] 62 31.794872 \n", + "Triangular face [HP:0000325] 62 31.794872 \n", + "Abnormal ear physiology [HP:0031704] 68 34.170854 \n", + "Hearing abnormality [HP:0000364] 68 34.170854 \n", + "Abnormal lip morphology [HP:0000159] 92 42.396313 \n", + "Abnormality of the philtrum [HP:0000288] 92 42.396313 \n", + "Abnormal upper lip morphology [HP:0000177] 92 42.396313 \n", + "Abnormal nasal morphology [HP:0005105] 99 46.478873 \n", + "Abnormality of the nose [HP:0000366] 99 46.478873 \n", + "Abnormal external nose morphology [HP:0010938] 99 46.478873 \n", + "Abnormal ear morphology [HP:0031703] 52 26.395939 \n", + "Atypical behavior [HP:0000708] 64 33.507853 \n", + "Short stature [HP:0004322] 101 43.913043 \n", + "Growth abnormality [HP:0001507] 101 43.913043 \n", + "Abnormality of body height [HP:0000002] 101 43.913043 \n", + "Growth delay [HP:0001510] 101 43.913043 \n", + "Abnormality of the dentition [HP:0000164] 159 67.088608 \n", + "Abnormal dental morphology [HP:0006482] 159 67.088608 \n", + "Macrodontia [HP:0001572] 159 67.088608 \n", + "Abnormality of the hand [HP:0001155] 134 55.371901 \n", + "Abnormality of the upper limb [HP:0002817] 134 55.371901 \n", + "Abnormality of limbs [HP:0040064] 134 55.371901 \n", + "Cognitive impairment [HP:0100543] 44 23.404255 \n", "\n", ">=1 allele of the variant 16_89284634_89284639_GTGTTT_G Yes \\\n", " Count Percent \n", - "Neurodevelopmental abnormality [HP:0012759] 21 8.677686 \n", - "Abnormal nervous system physiology [HP:0012638] 23 9.426230 \n", - "Abnormality of the nervous system [HP:0000707] 23 9.426230 \n", - "Intellectual disability [HP:0001249] 15 6.302521 \n", - "Phenotypic abnormality [HP:0000118] 31 12.350598 \n", - "All [HP:0000001] 31 12.350598 \n", - "Abnormality of mental function [HP:0011446] 19 7.916667 \n", - "Neurodevelopmental delay [HP:0012758] 14 6.862745 \n", - "Global developmental delay [HP:0001263] 14 6.862745 \n", - "Abnormality of the ear [HP:0000598] 10 4.784689 \n", - "Abnormality of the ocular adnexa [HP:0032039] 10 4.761905 \n", - "Abnormality of the orbital region [HP:0000315] 10 4.761905 \n", - "Abnormality of the integument [HP:0001574] 10 4.761905 \n", - "Abnormal skin adnexa morphology [HP:0011138] 10 4.761905 \n", - "Abnormal hair morphology [HP:0001595] 10 4.761905 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 10 4.761905 \n", - "Abnormality of the face [HP:0000271] 27 11.157025 \n", - "Abnormality of the head [HP:0000234] 27 11.157025 \n", - "Abnormality of head or neck [HP:0000152] 27 11.157025 \n", - "Abnormal oral morphology [HP:0031816] 25 10.416667 \n", - "Abnormality of the mouth [HP:0000153] 25 10.416667 \n", - "Abnormal oral cavity morphology [HP:0000163] 25 10.416667 \n", - "Abnormal facial shape [HP:0001999] 6 3.092784 \n", - "Triangular face [HP:0000325] 6 3.092784 \n", - "Hearing abnormality [HP:0000364] 7 3.535354 \n", - "Abnormal ear physiology [HP:0031704] 7 3.535354 \n", - "Abnormal upper lip morphology [HP:0000177] 11 5.092593 \n", - "Abnormality of the philtrum [HP:0000288] 11 5.092593 \n", - "Long philtrum [HP:0000343] 11 5.092593 \n", - "Abnormal lip morphology [HP:0000159] 11 5.092593 \n", - "Abnormality of the nose [HP:0000366] 13 6.132075 \n", - "Abnormal nasal morphology [HP:0005105] 13 6.132075 \n", - "Abnormal external nose morphology [HP:0010938] 13 6.132075 \n", - "Abnormal ear morphology [HP:0031703] 6 3.061224 \n", - "Atypical behavior [HP:0000708] 8 4.210526 \n", - "Growth delay [HP:0001510] 14 6.113537 \n", - "Abnormality of body height [HP:0000002] 14 6.113537 \n", - "Short stature [HP:0004322] 14 6.113537 \n", - "Growth abnormality [HP:0001507] 14 6.113537 \n", - "Abnormality of the dentition [HP:0000164] 23 9.745763 \n", - "Abnormal dental morphology [HP:0006482] 23 9.745763 \n", - "Macrodontia [HP:0001572] 23 9.745763 \n", - "Abnormality of limbs [HP:0040064] 22 9.128631 \n", - "Abnormality of the upper limb [HP:0002817] 22 9.128631 \n", - "Abnormality of the hand [HP:0001155] 22 9.128631 \n", - "Cognitive impairment [HP:0100543] 7 3.743316 \n", + "Neurodevelopmental abnormality [HP:0012759] 21 8.641975 \n", + "Intellectual disability [HP:0001249] 15 6.276151 \n", + "Abnormal nervous system physiology [HP:0012638] 23 9.387755 \n", + "Abnormality of the nervous system [HP:0000707] 23 9.387755 \n", + "Phenotypic abnormality [HP:0000118] 31 12.301587 \n", + "All [HP:0000001] 31 12.301587 \n", + "Abnormality of mental function [HP:0011446] 19 7.883817 \n", + "Abnormality of the orbital region [HP:0000315] 10 4.739336 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 10 4.739336 \n", + "Abnormal hair morphology [HP:0001595] 10 4.739336 \n", + "Abnormality of the integument [HP:0001574] 10 4.739336 \n", + "Abnormal skin adnexa morphology [HP:0011138] 10 4.739336 \n", + "Abnormality of the ocular adnexa [HP:0032039] 10 4.739336 \n", + "Global developmental delay [HP:0001263] 14 6.829268 \n", + "Neurodevelopmental delay [HP:0012758] 14 6.829268 \n", + "Abnormality of the ear [HP:0000598] 10 4.761905 \n", + "Abnormality of head or neck [HP:0000152] 27 11.111111 \n", + "Abnormality of the head [HP:0000234] 27 11.111111 \n", + "Abnormality of the face [HP:0000271] 27 11.111111 \n", + "Abnormality of the mouth [HP:0000153] 25 10.373444 \n", + "Abnormal oral cavity morphology [HP:0000163] 25 10.373444 \n", + "Abnormal oral morphology [HP:0031816] 25 10.373444 \n", + "Abnormal facial shape [HP:0001999] 6 3.076923 \n", + "Triangular face [HP:0000325] 6 3.076923 \n", + "Abnormal ear physiology [HP:0031704] 7 3.517588 \n", + "Hearing abnormality [HP:0000364] 7 3.517588 \n", + "Abnormal lip morphology [HP:0000159] 11 5.069124 \n", + "Abnormality of the philtrum [HP:0000288] 11 5.069124 \n", + "Abnormal upper lip morphology [HP:0000177] 11 5.069124 \n", + "Abnormal nasal morphology [HP:0005105] 13 6.103286 \n", + "Abnormality of the nose [HP:0000366] 13 6.103286 \n", + "Abnormal external nose morphology [HP:0010938] 13 6.103286 \n", + "Abnormal ear morphology [HP:0031703] 6 3.045685 \n", + "Atypical behavior [HP:0000708] 8 4.188482 \n", + "Short stature [HP:0004322] 14 6.086957 \n", + "Growth abnormality [HP:0001507] 14 6.086957 \n", + "Abnormality of body height [HP:0000002] 14 6.086957 \n", + "Growth delay [HP:0001510] 14 6.086957 \n", + "Abnormality of the dentition [HP:0000164] 23 9.704641 \n", + "Abnormal dental morphology [HP:0006482] 23 9.704641 \n", + "Macrodontia [HP:0001572] 23 9.704641 \n", + "Abnormality of the hand [HP:0001155] 22 9.090909 \n", + "Abnormality of the upper limb [HP:0002817] 22 9.090909 \n", + "Abnormality of limbs [HP:0040064] 22 9.090909 \n", + "Cognitive impairment [HP:0100543] 7 3.723404 \n", "\n", ">=1 allele of the variant 16_89284634_89284639_GTGTTT_G \\\n", " p value \n", - "Neurodevelopmental abnormality [HP:0012759] 0.007993 \n", - "Abnormal nervous system physiology [HP:0012638] 0.014355 \n", - "Abnormality of the nervous system [HP:0000707] 0.014355 \n", - "Intellectual disability [HP:0001249] 0.014702 \n", - "Phenotypic abnormality [HP:0000118] 0.046296 \n", - "All [HP:0000001] 0.046296 \n", - "Abnormality of mental function [HP:0011446] 0.048016 \n", - "Neurodevelopmental delay [HP:0012758] 0.056706 \n", - "Global developmental delay [HP:0001263] 0.056706 \n", - "Abnormality of the ear [HP:0000598] 0.066000 \n", - "Abnormality of the ocular adnexa [HP:0032039] 0.074632 \n", - "Abnormality of the orbital region [HP:0000315] 0.074632 \n", - "Abnormality of the integument [HP:0001574] 0.074632 \n", - "Abnormal skin adnexa morphology [HP:0011138] 0.074632 \n", - "Abnormal hair morphology [HP:0001595] 0.074632 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 0.074632 \n", - "Abnormality of the face [HP:0000271] 0.093495 \n", - "Abnormality of the head [HP:0000234] 0.093495 \n", - "Abnormality of head or neck [HP:0000152] 0.093495 \n", - "Abnormal oral morphology [HP:0031816] 0.109604 \n", - "Abnormality of the mouth [HP:0000153] 0.109604 \n", - "Abnormal oral cavity morphology [HP:0000163] 0.109604 \n", - "Abnormal facial shape [HP:0001999] 0.134129 \n", - "Triangular face [HP:0000325] 0.134129 \n", - "Hearing abnormality [HP:0000364] 0.205373 \n", - "Abnormal ear physiology [HP:0031704] 0.205373 \n", - "Abnormal upper lip morphology [HP:0000177] 0.238468 \n", - "Abnormality of the philtrum [HP:0000288] 0.238468 \n", - "Long philtrum [HP:0000343] 0.238468 \n", - "Abnormal lip morphology [HP:0000159] 0.238468 \n", - "Abnormality of the nose [HP:0000366] 0.242887 \n", - "Abnormal nasal morphology [HP:0005105] 0.242887 \n", - "Abnormal external nose morphology [HP:0010938] 0.242887 \n", - "Abnormal ear morphology [HP:0031703] 0.375674 \n", - "Atypical behavior [HP:0000708] 0.396639 \n", - "Growth delay [HP:0001510] 0.452237 \n", - "Abnormality of body height [HP:0000002] 0.452237 \n", - "Short stature [HP:0004322] 0.452237 \n", - "Growth abnormality [HP:0001507] 0.452237 \n", - "Abnormality of the dentition [HP:0000164] 0.651760 \n", - "Abnormal dental morphology [HP:0006482] 0.651760 \n", - "Macrodontia [HP:0001572] 0.651760 \n", - "Abnormality of limbs [HP:0040064] 0.847288 \n", - "Abnormality of the upper limb [HP:0002817] 0.847288 \n", - "Abnormality of the hand [HP:0001155] 0.847288 \n", + "Neurodevelopmental abnormality [HP:0012759] 0.014389 \n", + "Intellectual disability [HP:0001249] 0.015381 \n", + "Abnormal nervous system physiology [HP:0012638] 0.016113 \n", + "Abnormality of the nervous system [HP:0000707] 0.016113 \n", + "Phenotypic abnormality [HP:0000118] 0.045945 \n", + "All [HP:0000001] 0.045945 \n", + "Abnormality of mental function [HP:0011446] 0.050034 \n", + "Abnormality of the orbital region [HP:0000315] 0.050625 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 0.050625 \n", + "Abnormal hair morphology [HP:0001595] 0.050625 \n", + "Abnormality of the integument [HP:0001574] 0.050625 \n", + "Abnormal skin adnexa morphology [HP:0011138] 0.050625 \n", + "Abnormality of the ocular adnexa [HP:0032039] 0.050625 \n", + "Global developmental delay [HP:0001263] 0.058015 \n", + "Neurodevelopmental delay [HP:0012758] 0.058015 \n", + "Abnormality of the ear [HP:0000598] 0.065729 \n", + "Abnormality of head or neck [HP:0000152] 0.092993 \n", + "Abnormality of the head [HP:0000234] 0.092993 \n", + "Abnormality of the face [HP:0000271] 0.092993 \n", + "Abnormality of the mouth [HP:0000153] 0.117228 \n", + "Abnormal oral cavity morphology [HP:0000163] 0.117228 \n", + "Abnormal oral morphology [HP:0031816] 0.117228 \n", + "Abnormal facial shape [HP:0001999] 0.134696 \n", + "Triangular face [HP:0000325] 0.134696 \n", + "Abnormal ear physiology [HP:0031704] 0.147568 \n", + "Hearing abnormality [HP:0000364] 0.147568 \n", + "Abnormal lip morphology [HP:0000159] 0.239690 \n", + "Abnormality of the philtrum [HP:0000288] 0.239690 \n", + "Abnormal upper lip morphology [HP:0000177] 0.239690 \n", + "Abnormal nasal morphology [HP:0005105] 0.244040 \n", + "Abnormality of the nose [HP:0000366] 0.244040 \n", + "Abnormal external nose morphology [HP:0010938] 0.244040 \n", + "Abnormal ear morphology [HP:0031703] 0.376567 \n", + "Atypical behavior [HP:0000708] 0.398051 \n", + "Short stature [HP:0004322] 0.568154 \n", + "Growth abnormality [HP:0001507] 0.568154 \n", + "Abnormality of body height [HP:0000002] 0.568154 \n", + "Growth delay [HP:0001510] 0.568154 \n", + "Abnormality of the dentition [HP:0000164] 0.819515 \n", + "Abnormal dental morphology [HP:0006482] 0.819515 \n", + "Macrodontia [HP:0001572] 0.819515 \n", + "Abnormality of the hand [HP:0001155] 0.846725 \n", + "Abnormality of the upper limb [HP:0002817] 0.846725 \n", + "Abnormality of limbs [HP:0040064] 0.846725 \n", "Cognitive impairment [HP:0100543] 1.000000 \n", "\n", ">=1 allele of the variant 16_89284634_89284639_GTGTTT_G \n", " Corrected p value \n", - "Neurodevelopmental abnormality [HP:0012759] 0.169079 \n", - "Abnormal nervous system physiology [HP:0012638] 0.169079 \n", - "Abnormality of the nervous system [HP:0000707] 0.169079 \n", - "Intellectual disability [HP:0001249] 0.169079 \n", - "Phenotypic abnormality [HP:0000118] 0.214567 \n", - "All [HP:0000001] 0.214567 \n", - "Abnormality of mental function [HP:0011446] 0.214567 \n", - "Neurodevelopmental delay [HP:0012758] 0.214567 \n", - "Global developmental delay [HP:0001263] 0.214567 \n", - "Abnormality of the ear [HP:0000598] 0.214567 \n", - "Abnormality of the ocular adnexa [HP:0032039] 0.214567 \n", - "Abnormality of the orbital region [HP:0000315] 0.214567 \n", - "Abnormality of the integument [HP:0001574] 0.214567 \n", - "Abnormal skin adnexa morphology [HP:0011138] 0.214567 \n", - "Abnormal hair morphology [HP:0001595] 0.214567 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 0.214567 \n", - "Abnormality of the face [HP:0000271] 0.226357 \n", - "Abnormality of the head [HP:0000234] 0.226357 \n", - "Abnormality of head or neck [HP:0000152] 0.226357 \n", - "Abnormal oral morphology [HP:0031816] 0.229172 \n", - "Abnormality of the mouth [HP:0000153] 0.229172 \n", - "Abnormal oral cavity morphology [HP:0000163] 0.229172 \n", - "Abnormal facial shape [HP:0001999] 0.257080 \n", - "Triangular face [HP:0000325] 0.257080 \n", - "Hearing abnormality [HP:0000364] 0.338570 \n", - "Abnormal ear physiology [HP:0031704] 0.338570 \n", - "Abnormal upper lip morphology [HP:0000177] 0.338570 \n", - "Abnormality of the philtrum [HP:0000288] 0.338570 \n", - "Long philtrum [HP:0000343] 0.338570 \n", - "Abnormal lip morphology [HP:0000159] 0.338570 \n", - "Abnormality of the nose [HP:0000366] 0.338570 \n", - "Abnormal nasal morphology [HP:0005105] 0.338570 \n", - "Abnormal external nose morphology [HP:0010938] 0.338570 \n", - "Abnormal ear morphology [HP:0031703] 0.508265 \n", - "Atypical behavior [HP:0000708] 0.521297 \n", - "Growth delay [HP:0001510] 0.533408 \n", - "Abnormality of body height [HP:0000002] 0.533408 \n", - "Short stature [HP:0004322] 0.533408 \n", - "Growth abnormality [HP:0001507] 0.533408 \n", - "Abnormality of the dentition [HP:0000164] 0.713833 \n", - "Abnormal dental morphology [HP:0006482] 0.713833 \n", - "Macrodontia [HP:0001572] 0.713833 \n", - "Abnormality of limbs [HP:0040064] 0.866116 \n", - "Abnormality of the upper limb [HP:0002817] 0.866116 \n", - "Abnormality of the hand [HP:0001155] 0.866116 \n", + "Neurodevelopmental abnormality [HP:0012759] 0.174046 \n", + "Intellectual disability [HP:0001249] 0.174046 \n", + "Abnormal nervous system physiology [HP:0012638] 0.174046 \n", + "Abnormality of the nervous system [HP:0000707] 0.174046 \n", + "Phenotypic abnormality [HP:0000118] 0.174046 \n", + "All [HP:0000001] 0.174046 \n", + "Abnormality of mental function [HP:0011446] 0.174046 \n", + "Abnormality of the orbital region [HP:0000315] 0.174046 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 0.174046 \n", + "Abnormal hair morphology [HP:0001595] 0.174046 \n", + "Abnormality of the integument [HP:0001574] 0.174046 \n", + "Abnormal skin adnexa morphology [HP:0011138] 0.174046 \n", + "Abnormality of the ocular adnexa [HP:0032039] 0.174046 \n", + "Global developmental delay [HP:0001263] 0.174046 \n", + "Neurodevelopmental delay [HP:0012758] 0.174046 \n", + "Abnormality of the ear [HP:0000598] 0.184863 \n", + "Abnormality of head or neck [HP:0000152] 0.220246 \n", + "Abnormality of the head [HP:0000234] 0.220246 \n", + "Abnormality of the face [HP:0000271] 0.220246 \n", + "Abnormality of the mouth [HP:0000153] 0.239785 \n", + "Abnormal oral cavity morphology [HP:0000163] 0.239785 \n", + "Abnormal oral morphology [HP:0031816] 0.239785 \n", + "Abnormal facial shape [HP:0001999] 0.252556 \n", + "Triangular face [HP:0000325] 0.252556 \n", + "Abnormal ear physiology [HP:0031704] 0.255407 \n", + "Hearing abnormality [HP:0000364] 0.255407 \n", + "Abnormal lip morphology [HP:0000159] 0.343181 \n", + "Abnormality of the philtrum [HP:0000288] 0.343181 \n", + "Abnormal upper lip morphology [HP:0000177] 0.343181 \n", + "Abnormal nasal morphology [HP:0005105] 0.343181 \n", + "Abnormality of the nose [HP:0000366] 0.343181 \n", + "Abnormal external nose morphology [HP:0010938] 0.343181 \n", + "Abnormal ear morphology [HP:0031703] 0.513501 \n", + "Atypical behavior [HP:0000708] 0.526832 \n", + "Short stature [HP:0004322] 0.672813 \n", + "Growth abnormality [HP:0001507] 0.672813 \n", + "Abnormality of body height [HP:0000002] 0.672813 \n", + "Growth delay [HP:0001510] 0.672813 \n", + "Abnormality of the dentition [HP:0000164] 0.865969 \n", + "Abnormal dental morphology [HP:0006482] 0.865969 \n", + "Macrodontia [HP:0001572] 0.865969 \n", + "Abnormality of the hand [HP:0001155] 0.865969 \n", + "Abnormality of the upper limb [HP:0002817] 0.865969 \n", + "Abnormality of limbs [HP:0040064] 0.865969 \n", "Cognitive impairment [HP:0100543] 1.000000 " ] }, @@ -2010,7 +1988,7 @@ " 1.0\n", " \n", " \n", - " Hearing abnormality [HP:0000364]\n", + " Abnormal ear physiology [HP:0031704]\n", " 3\n", " 8.333333\n", " 7\n", @@ -2019,7 +1997,7 @@ " 1.0\n", " \n", " \n", - " Abnormal ear physiology [HP:0031704]\n", + " Hearing abnormality [HP:0000364]\n", " 3\n", " 8.333333\n", " 7\n", @@ -2037,7 +2015,7 @@ " 1.0\n", " \n", " \n", - " Abnormality of the hand [HP:0001155]\n", + " Abnormality of limbs [HP:0040064]\n", " 8\n", " 18.604651\n", " 22\n", @@ -2046,7 +2024,7 @@ " 1.0\n", " \n", " \n", - " Abnormality of the upper limb [HP:0002817]\n", + " Abnormality of the hand [HP:0001155]\n", " 8\n", " 18.604651\n", " 22\n", @@ -2055,7 +2033,7 @@ " 1.0\n", " \n", " \n", - " Abnormality of limbs [HP:0040064]\n", + " Abnormality of the upper limb [HP:0002817]\n", " 8\n", " 18.604651\n", " 22\n", @@ -2064,7 +2042,7 @@ " 1.0\n", " \n", " \n", - " Abnormal external nose morphology [HP:0010938]\n", + " Abnormality of the nose [HP:0000366]\n", " 5\n", " 12.500000\n", " 13\n", @@ -2082,7 +2060,7 @@ " 1.0\n", " \n", " \n", - " Abnormality of the nose [HP:0000366]\n", + " Abnormal external nose morphology [HP:0010938]\n", " 5\n", " 12.500000\n", " 13\n", @@ -2100,7 +2078,7 @@ " 1.0\n", " \n", " \n", - " Long philtrum [HP:0000343]\n", + " Abnormal upper lip morphology [HP:0000177]\n", " 4\n", " 10.256410\n", " 11\n", @@ -2109,7 +2087,7 @@ " 1.0\n", " \n", " \n", - " Abnormal upper lip morphology [HP:0000177]\n", + " Abnormality of the philtrum [HP:0000288]\n", " 4\n", " 10.256410\n", " 11\n", @@ -2118,16 +2096,16 @@ " 1.0\n", " \n", " \n", - " Abnormality of the philtrum [HP:0000288]\n", - " 4\n", - " 10.256410\n", - " 11\n", - " 28.205128\n", - " 0.711011\n", + " Triangular face [HP:0000325]\n", + " 2\n", + " 5.555556\n", + " 6\n", + " 16.666667\n", + " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormal oral cavity morphology [HP:0000163]\n", + " Abnormality of the mouth [HP:0000153]\n", " 8\n", " 18.604651\n", " 25\n", @@ -2136,7 +2114,7 @@ " 1.0\n", " \n", " \n", - " Abnormality of the mouth [HP:0000153]\n", + " Abnormal oral morphology [HP:0031816]\n", " 8\n", " 18.604651\n", " 25\n", @@ -2145,79 +2123,79 @@ " 1.0\n", " \n", " \n", - " Abnormality of the dentition [HP:0000164]\n", + " Abnormal oral cavity morphology [HP:0000163]\n", " 8\n", - " 19.512195\n", - " 23\n", - " 56.097561\n", + " 18.604651\n", + " 25\n", + " 58.139535\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Intellectual disability [HP:0001249]\n", - " 5\n", - " 11.904762\n", - " 15\n", - " 35.714286\n", + " Abnormality of the orbital region [HP:0000315]\n", + " 3\n", + " 7.692308\n", + " 10\n", + " 25.641026\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormality of the head [HP:0000234]\n", - " 9\n", - " 20.930233\n", - " 27\n", - " 62.790698\n", + " Abnormality of the integument [HP:0001574]\n", + " 3\n", + " 7.692308\n", + " 10\n", + " 25.641026\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormality of head or neck [HP:0000152]\n", - " 9\n", - " 20.930233\n", - " 27\n", - " 62.790698\n", + " Abnormality of the ocular adnexa [HP:0032039]\n", + " 3\n", + " 7.692308\n", + " 10\n", + " 25.641026\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Triangular face [HP:0000325]\n", - " 2\n", - " 5.555556\n", - " 6\n", - " 16.666667\n", + " Abnormal skin adnexa morphology [HP:0011138]\n", + " 3\n", + " 7.692308\n", + " 10\n", + " 25.641026\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormal facial shape [HP:0001999]\n", - " 2\n", - " 5.555556\n", - " 6\n", - " 16.666667\n", + " Abnormal ocular adnexa morphology [HP:0030669]\n", + " 3\n", + " 7.692308\n", + " 10\n", + " 25.641026\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormal dental morphology [HP:0006482]\n", - " 8\n", - " 19.512195\n", - " 23\n", - " 56.097561\n", + " Abnormal hair morphology [HP:0001595]\n", + " 3\n", + " 7.692308\n", + " 10\n", + " 25.641026\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormality of the face [HP:0000271]\n", - " 9\n", - " 20.930233\n", - " 27\n", - " 62.790698\n", + " All [HP:0000001]\n", + " 10\n", + " 23.255814\n", + " 31\n", + " 72.093023\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Macrodontia [HP:0001572]\n", + " Abnormality of the dentition [HP:0000164]\n", " 8\n", " 19.512195\n", " 23\n", @@ -2226,15 +2204,6 @@ " 1.0\n", " \n", " \n", - " Abnormal ear morphology [HP:0031703]\n", - " 1\n", - " 2.777778\n", - " 6\n", - " 16.666667\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", " Phenotypic abnormality [HP:0000118]\n", " 10\n", " 23.255814\n", @@ -2244,6 +2213,24 @@ " 1.0\n", " \n", " \n", + " Abnormality of the head [HP:0000234]\n", + " 9\n", + " 20.930233\n", + " 27\n", + " 62.790698\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormality of the face [HP:0000271]\n", + " 9\n", + " 20.930233\n", + " 27\n", + " 62.790698\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", " Abnormality of the nervous system [HP:0000707]\n", " 7\n", " 16.279070\n", @@ -2253,20 +2240,20 @@ " 1.0\n", " \n", " \n", - " Abnormal nervous system physiology [HP:0012638]\n", - " 7\n", - " 16.279070\n", - " 23\n", - " 53.488372\n", + " Global developmental delay [HP:0001263]\n", + " 4\n", + " 10.526316\n", + " 14\n", + " 36.842105\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Neurodevelopmental abnormality [HP:0012759]\n", - " 6\n", - " 13.953488\n", - " 21\n", - " 48.837209\n", + " Intellectual disability [HP:0001249]\n", + " 5\n", + " 11.904762\n", + " 15\n", + " 35.714286\n", " 1.000000\n", " 1.0\n", " \n", @@ -2280,101 +2267,83 @@ " 1.0\n", " \n", " \n", - " Abnormal oral morphology [HP:0031816]\n", - " 8\n", - " 18.604651\n", - " 25\n", - " 58.139535\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of the orbital region [HP:0000315]\n", - " 3\n", - " 7.692308\n", - " 10\n", - " 25.641026\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of the integument [HP:0001574]\n", - " 3\n", - " 7.692308\n", - " 10\n", - " 25.641026\n", + " Neurodevelopmental delay [HP:0012758]\n", + " 4\n", + " 10.526316\n", + " 14\n", + " 36.842105\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormality of the ocular adnexa [HP:0032039]\n", - " 3\n", - " 7.692308\n", - " 10\n", - " 25.641026\n", + " Abnormal nervous system physiology [HP:0012638]\n", + " 7\n", + " 16.279070\n", + " 23\n", + " 53.488372\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormal skin adnexa morphology [HP:0011138]\n", - " 3\n", - " 7.692308\n", - " 10\n", - " 25.641026\n", + " Macrodontia [HP:0001572]\n", + " 8\n", + " 19.512195\n", + " 23\n", + " 56.097561\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormal ocular adnexa morphology [HP:0030669]\n", - " 3\n", - " 7.692308\n", - " 10\n", - " 25.641026\n", + " Atypical behavior [HP:0000708]\n", + " 2\n", + " 5.555556\n", + " 8\n", + " 22.222222\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Abnormal hair morphology [HP:0001595]\n", - " 3\n", - " 7.692308\n", - " 10\n", - " 25.641026\n", + " Abnormal dental morphology [HP:0006482]\n", + " 8\n", + " 19.512195\n", + " 23\n", + " 56.097561\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Neurodevelopmental delay [HP:0012758]\n", - " 4\n", - " 10.526316\n", - " 14\n", - " 36.842105\n", + " Abnormal ear morphology [HP:0031703]\n", + " 1\n", + " 2.777778\n", + " 6\n", + " 16.666667\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Global developmental delay [HP:0001263]\n", - " 4\n", - " 10.526316\n", - " 14\n", - " 36.842105\n", + " Abnormal facial shape [HP:0001999]\n", + " 2\n", + " 5.555556\n", + " 6\n", + " 16.666667\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " All [HP:0000001]\n", - " 10\n", - " 23.255814\n", - " 31\n", - " 72.093023\n", + " Abnormality of head or neck [HP:0000152]\n", + " 9\n", + " 20.930233\n", + " 27\n", + " 62.790698\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Atypical behavior [HP:0000708]\n", - " 2\n", - " 5.555556\n", - " 8\n", - " 22.222222\n", + " Neurodevelopmental abnormality [HP:0012759]\n", + " 6\n", + " 13.953488\n", + " 21\n", + " 48.837209\n", " 1.000000\n", " 1.0\n", " \n", @@ -2390,47 +2359,46 @@ "Abnormality of body height [HP:0000002] 5 \n", "Growth delay [HP:0001510] 5 \n", "Growth abnormality [HP:0001507] 5 \n", - "Hearing abnormality [HP:0000364] 3 \n", "Abnormal ear physiology [HP:0031704] 3 \n", + "Hearing abnormality [HP:0000364] 3 \n", "Abnormality of the ear [HP:0000598] 4 \n", + "Abnormality of limbs [HP:0040064] 8 \n", "Abnormality of the hand [HP:0001155] 8 \n", "Abnormality of the upper limb [HP:0002817] 8 \n", - "Abnormality of limbs [HP:0040064] 8 \n", - "Abnormal external nose morphology [HP:0010938] 5 \n", - "Abnormal nasal morphology [HP:0005105] 5 \n", "Abnormality of the nose [HP:0000366] 5 \n", + "Abnormal nasal morphology [HP:0005105] 5 \n", + "Abnormal external nose morphology [HP:0010938] 5 \n", "Abnormal lip morphology [HP:0000159] 4 \n", - "Long philtrum [HP:0000343] 4 \n", "Abnormal upper lip morphology [HP:0000177] 4 \n", "Abnormality of the philtrum [HP:0000288] 4 \n", - "Abnormal oral cavity morphology [HP:0000163] 8 \n", - "Abnormality of the mouth [HP:0000153] 8 \n", - "Abnormality of the dentition [HP:0000164] 8 \n", - "Intellectual disability [HP:0001249] 5 \n", - "Abnormality of the head [HP:0000234] 9 \n", - "Abnormality of head or neck [HP:0000152] 9 \n", "Triangular face [HP:0000325] 2 \n", - "Abnormal facial shape [HP:0001999] 2 \n", - "Abnormal dental morphology [HP:0006482] 8 \n", - "Abnormality of the face [HP:0000271] 9 \n", - "Macrodontia [HP:0001572] 8 \n", - "Abnormal ear morphology [HP:0031703] 1 \n", - "Phenotypic abnormality [HP:0000118] 10 \n", - "Abnormality of the nervous system [HP:0000707] 7 \n", - "Abnormal nervous system physiology [HP:0012638] 7 \n", - "Neurodevelopmental abnormality [HP:0012759] 6 \n", - "Abnormality of mental function [HP:0011446] 6 \n", + "Abnormality of the mouth [HP:0000153] 8 \n", "Abnormal oral morphology [HP:0031816] 8 \n", + "Abnormal oral cavity morphology [HP:0000163] 8 \n", "Abnormality of the orbital region [HP:0000315] 3 \n", "Abnormality of the integument [HP:0001574] 3 \n", "Abnormality of the ocular adnexa [HP:0032039] 3 \n", "Abnormal skin adnexa morphology [HP:0011138] 3 \n", "Abnormal ocular adnexa morphology [HP:0030669] 3 \n", "Abnormal hair morphology [HP:0001595] 3 \n", - "Neurodevelopmental delay [HP:0012758] 4 \n", - "Global developmental delay [HP:0001263] 4 \n", "All [HP:0000001] 10 \n", + "Abnormality of the dentition [HP:0000164] 8 \n", + "Phenotypic abnormality [HP:0000118] 10 \n", + "Abnormality of the head [HP:0000234] 9 \n", + "Abnormality of the face [HP:0000271] 9 \n", + "Abnormality of the nervous system [HP:0000707] 7 \n", + "Global developmental delay [HP:0001263] 4 \n", + "Intellectual disability [HP:0001249] 5 \n", + "Abnormality of mental function [HP:0011446] 6 \n", + "Neurodevelopmental delay [HP:0012758] 4 \n", + "Abnormal nervous system physiology [HP:0012638] 7 \n", + "Macrodontia [HP:0001572] 8 \n", "Atypical behavior [HP:0000708] 2 \n", + "Abnormal dental morphology [HP:0006482] 8 \n", + "Abnormal ear morphology [HP:0031703] 1 \n", + "Abnormal facial shape [HP:0001999] 2 \n", + "Abnormality of head or neck [HP:0000152] 9 \n", + "Neurodevelopmental abnormality [HP:0012759] 6 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G \\\n", " Percent \n", @@ -2439,47 +2407,46 @@ "Abnormality of body height [HP:0000002] 12.500000 \n", "Growth delay [HP:0001510] 12.500000 \n", "Growth abnormality [HP:0001507] 12.500000 \n", - "Hearing abnormality [HP:0000364] 8.333333 \n", "Abnormal ear physiology [HP:0031704] 8.333333 \n", + "Hearing abnormality [HP:0000364] 8.333333 \n", "Abnormality of the ear [HP:0000598] 11.111111 \n", + "Abnormality of limbs [HP:0040064] 18.604651 \n", "Abnormality of the hand [HP:0001155] 18.604651 \n", "Abnormality of the upper limb [HP:0002817] 18.604651 \n", - "Abnormality of limbs [HP:0040064] 18.604651 \n", - "Abnormal external nose morphology [HP:0010938] 12.500000 \n", - "Abnormal nasal morphology [HP:0005105] 12.500000 \n", "Abnormality of the nose [HP:0000366] 12.500000 \n", + "Abnormal nasal morphology [HP:0005105] 12.500000 \n", + "Abnormal external nose morphology [HP:0010938] 12.500000 \n", "Abnormal lip morphology [HP:0000159] 10.256410 \n", - "Long philtrum [HP:0000343] 10.256410 \n", "Abnormal upper lip morphology [HP:0000177] 10.256410 \n", "Abnormality of the philtrum [HP:0000288] 10.256410 \n", - "Abnormal oral cavity morphology [HP:0000163] 18.604651 \n", - "Abnormality of the mouth [HP:0000153] 18.604651 \n", - "Abnormality of the dentition [HP:0000164] 19.512195 \n", - "Intellectual disability [HP:0001249] 11.904762 \n", - "Abnormality of the head [HP:0000234] 20.930233 \n", - "Abnormality of head or neck [HP:0000152] 20.930233 \n", "Triangular face [HP:0000325] 5.555556 \n", - "Abnormal facial shape [HP:0001999] 5.555556 \n", - "Abnormal dental morphology [HP:0006482] 19.512195 \n", - "Abnormality of the face [HP:0000271] 20.930233 \n", - "Macrodontia [HP:0001572] 19.512195 \n", - "Abnormal ear morphology [HP:0031703] 2.777778 \n", - "Phenotypic abnormality [HP:0000118] 23.255814 \n", - "Abnormality of the nervous system [HP:0000707] 16.279070 \n", - "Abnormal nervous system physiology [HP:0012638] 16.279070 \n", - "Neurodevelopmental abnormality [HP:0012759] 13.953488 \n", - "Abnormality of mental function [HP:0011446] 14.285714 \n", + "Abnormality of the mouth [HP:0000153] 18.604651 \n", "Abnormal oral morphology [HP:0031816] 18.604651 \n", + "Abnormal oral cavity morphology [HP:0000163] 18.604651 \n", "Abnormality of the orbital region [HP:0000315] 7.692308 \n", "Abnormality of the integument [HP:0001574] 7.692308 \n", "Abnormality of the ocular adnexa [HP:0032039] 7.692308 \n", "Abnormal skin adnexa morphology [HP:0011138] 7.692308 \n", "Abnormal ocular adnexa morphology [HP:0030669] 7.692308 \n", "Abnormal hair morphology [HP:0001595] 7.692308 \n", - "Neurodevelopmental delay [HP:0012758] 10.526316 \n", - "Global developmental delay [HP:0001263] 10.526316 \n", "All [HP:0000001] 23.255814 \n", + "Abnormality of the dentition [HP:0000164] 19.512195 \n", + "Phenotypic abnormality [HP:0000118] 23.255814 \n", + "Abnormality of the head [HP:0000234] 20.930233 \n", + "Abnormality of the face [HP:0000271] 20.930233 \n", + "Abnormality of the nervous system [HP:0000707] 16.279070 \n", + "Global developmental delay [HP:0001263] 10.526316 \n", + "Intellectual disability [HP:0001249] 11.904762 \n", + "Abnormality of mental function [HP:0011446] 14.285714 \n", + "Neurodevelopmental delay [HP:0012758] 10.526316 \n", + "Abnormal nervous system physiology [HP:0012638] 16.279070 \n", + "Macrodontia [HP:0001572] 19.512195 \n", "Atypical behavior [HP:0000708] 5.555556 \n", + "Abnormal dental morphology [HP:0006482] 19.512195 \n", + "Abnormal ear morphology [HP:0031703] 2.777778 \n", + "Abnormal facial shape [HP:0001999] 5.555556 \n", + "Abnormality of head or neck [HP:0000152] 20.930233 \n", + "Neurodevelopmental abnormality [HP:0012759] 13.953488 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G Second \\\n", " Count \n", @@ -2488,47 +2455,46 @@ "Abnormality of body height [HP:0000002] 14 \n", "Growth delay [HP:0001510] 14 \n", "Growth abnormality [HP:0001507] 14 \n", - "Hearing abnormality [HP:0000364] 7 \n", "Abnormal ear physiology [HP:0031704] 7 \n", + "Hearing abnormality [HP:0000364] 7 \n", "Abnormality of the ear [HP:0000598] 10 \n", + "Abnormality of limbs [HP:0040064] 22 \n", "Abnormality of the hand [HP:0001155] 22 \n", "Abnormality of the upper limb [HP:0002817] 22 \n", - "Abnormality of limbs [HP:0040064] 22 \n", - "Abnormal external nose morphology [HP:0010938] 13 \n", - "Abnormal nasal morphology [HP:0005105] 13 \n", "Abnormality of the nose [HP:0000366] 13 \n", + "Abnormal nasal morphology [HP:0005105] 13 \n", + "Abnormal external nose morphology [HP:0010938] 13 \n", "Abnormal lip morphology [HP:0000159] 11 \n", - "Long philtrum [HP:0000343] 11 \n", "Abnormal upper lip morphology [HP:0000177] 11 \n", "Abnormality of the philtrum [HP:0000288] 11 \n", - "Abnormal oral cavity morphology [HP:0000163] 25 \n", - "Abnormality of the mouth [HP:0000153] 25 \n", - "Abnormality of the dentition [HP:0000164] 23 \n", - "Intellectual disability [HP:0001249] 15 \n", - "Abnormality of the head [HP:0000234] 27 \n", - "Abnormality of head or neck [HP:0000152] 27 \n", "Triangular face [HP:0000325] 6 \n", - "Abnormal facial shape [HP:0001999] 6 \n", - "Abnormal dental morphology [HP:0006482] 23 \n", - "Abnormality of the face [HP:0000271] 27 \n", - "Macrodontia [HP:0001572] 23 \n", - "Abnormal ear morphology [HP:0031703] 6 \n", - "Phenotypic abnormality [HP:0000118] 31 \n", - "Abnormality of the nervous system [HP:0000707] 23 \n", - "Abnormal nervous system physiology [HP:0012638] 23 \n", - "Neurodevelopmental abnormality [HP:0012759] 21 \n", - "Abnormality of mental function [HP:0011446] 19 \n", + "Abnormality of the mouth [HP:0000153] 25 \n", "Abnormal oral morphology [HP:0031816] 25 \n", + "Abnormal oral cavity morphology [HP:0000163] 25 \n", "Abnormality of the orbital region [HP:0000315] 10 \n", "Abnormality of the integument [HP:0001574] 10 \n", "Abnormality of the ocular adnexa [HP:0032039] 10 \n", "Abnormal skin adnexa morphology [HP:0011138] 10 \n", "Abnormal ocular adnexa morphology [HP:0030669] 10 \n", "Abnormal hair morphology [HP:0001595] 10 \n", - "Neurodevelopmental delay [HP:0012758] 14 \n", - "Global developmental delay [HP:0001263] 14 \n", "All [HP:0000001] 31 \n", + "Abnormality of the dentition [HP:0000164] 23 \n", + "Phenotypic abnormality [HP:0000118] 31 \n", + "Abnormality of the head [HP:0000234] 27 \n", + "Abnormality of the face [HP:0000271] 27 \n", + "Abnormality of the nervous system [HP:0000707] 23 \n", + "Global developmental delay [HP:0001263] 14 \n", + "Intellectual disability [HP:0001249] 15 \n", + "Abnormality of mental function [HP:0011446] 19 \n", + "Neurodevelopmental delay [HP:0012758] 14 \n", + "Abnormal nervous system physiology [HP:0012638] 23 \n", + "Macrodontia [HP:0001572] 23 \n", "Atypical behavior [HP:0000708] 8 \n", + "Abnormal dental morphology [HP:0006482] 23 \n", + "Abnormal ear morphology [HP:0031703] 6 \n", + "Abnormal facial shape [HP:0001999] 6 \n", + "Abnormality of head or neck [HP:0000152] 27 \n", + "Neurodevelopmental abnormality [HP:0012759] 21 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G \\\n", " Percent \n", @@ -2537,47 +2503,46 @@ "Abnormality of body height [HP:0000002] 35.000000 \n", "Growth delay [HP:0001510] 35.000000 \n", "Growth abnormality [HP:0001507] 35.000000 \n", - "Hearing abnormality [HP:0000364] 19.444444 \n", "Abnormal ear physiology [HP:0031704] 19.444444 \n", + "Hearing abnormality [HP:0000364] 19.444444 \n", "Abnormality of the ear [HP:0000598] 27.777778 \n", + "Abnormality of limbs [HP:0040064] 51.162791 \n", "Abnormality of the hand [HP:0001155] 51.162791 \n", "Abnormality of the upper limb [HP:0002817] 51.162791 \n", - "Abnormality of limbs [HP:0040064] 51.162791 \n", - "Abnormal external nose morphology [HP:0010938] 32.500000 \n", - "Abnormal nasal morphology [HP:0005105] 32.500000 \n", "Abnormality of the nose [HP:0000366] 32.500000 \n", + "Abnormal nasal morphology [HP:0005105] 32.500000 \n", + "Abnormal external nose morphology [HP:0010938] 32.500000 \n", "Abnormal lip morphology [HP:0000159] 28.205128 \n", - "Long philtrum [HP:0000343] 28.205128 \n", "Abnormal upper lip morphology [HP:0000177] 28.205128 \n", "Abnormality of the philtrum [HP:0000288] 28.205128 \n", - "Abnormal oral cavity morphology [HP:0000163] 58.139535 \n", - "Abnormality of the mouth [HP:0000153] 58.139535 \n", - "Abnormality of the dentition [HP:0000164] 56.097561 \n", - "Intellectual disability [HP:0001249] 35.714286 \n", - "Abnormality of the head [HP:0000234] 62.790698 \n", - "Abnormality of head or neck [HP:0000152] 62.790698 \n", "Triangular face [HP:0000325] 16.666667 \n", - "Abnormal facial shape [HP:0001999] 16.666667 \n", - "Abnormal dental morphology [HP:0006482] 56.097561 \n", - "Abnormality of the face [HP:0000271] 62.790698 \n", - "Macrodontia [HP:0001572] 56.097561 \n", - "Abnormal ear morphology [HP:0031703] 16.666667 \n", - "Phenotypic abnormality [HP:0000118] 72.093023 \n", - "Abnormality of the nervous system [HP:0000707] 53.488372 \n", - "Abnormal nervous system physiology [HP:0012638] 53.488372 \n", - "Neurodevelopmental abnormality [HP:0012759] 48.837209 \n", - "Abnormality of mental function [HP:0011446] 45.238095 \n", + "Abnormality of the mouth [HP:0000153] 58.139535 \n", "Abnormal oral morphology [HP:0031816] 58.139535 \n", + "Abnormal oral cavity morphology [HP:0000163] 58.139535 \n", "Abnormality of the orbital region [HP:0000315] 25.641026 \n", "Abnormality of the integument [HP:0001574] 25.641026 \n", "Abnormality of the ocular adnexa [HP:0032039] 25.641026 \n", "Abnormal skin adnexa morphology [HP:0011138] 25.641026 \n", "Abnormal ocular adnexa morphology [HP:0030669] 25.641026 \n", "Abnormal hair morphology [HP:0001595] 25.641026 \n", - "Neurodevelopmental delay [HP:0012758] 36.842105 \n", - "Global developmental delay [HP:0001263] 36.842105 \n", "All [HP:0000001] 72.093023 \n", + "Abnormality of the dentition [HP:0000164] 56.097561 \n", + "Phenotypic abnormality [HP:0000118] 72.093023 \n", + "Abnormality of the head [HP:0000234] 62.790698 \n", + "Abnormality of the face [HP:0000271] 62.790698 \n", + "Abnormality of the nervous system [HP:0000707] 53.488372 \n", + "Global developmental delay [HP:0001263] 36.842105 \n", + "Intellectual disability [HP:0001249] 35.714286 \n", + "Abnormality of mental function [HP:0011446] 45.238095 \n", + "Neurodevelopmental delay [HP:0012758] 36.842105 \n", + "Abnormal nervous system physiology [HP:0012638] 53.488372 \n", + "Macrodontia [HP:0001572] 56.097561 \n", "Atypical behavior [HP:0000708] 22.222222 \n", + "Abnormal dental morphology [HP:0006482] 56.097561 \n", + "Abnormal ear morphology [HP:0031703] 16.666667 \n", + "Abnormal facial shape [HP:0001999] 16.666667 \n", + "Abnormality of head or neck [HP:0000152] 62.790698 \n", + "Neurodevelopmental abnormality [HP:0012759] 48.837209 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G \\\n", " p value \n", @@ -2586,47 +2551,46 @@ "Abnormality of body height [HP:0000002] 0.441958 \n", "Growth delay [HP:0001510] 0.441958 \n", "Growth abnormality [HP:0001507] 0.441958 \n", - "Hearing abnormality [HP:0000364] 0.657626 \n", "Abnormal ear physiology [HP:0031704] 0.657626 \n", + "Hearing abnormality [HP:0000364] 0.657626 \n", "Abnormality of the ear [HP:0000598] 0.683230 \n", + "Abnormality of limbs [HP:0040064] 0.696329 \n", "Abnormality of the hand [HP:0001155] 0.696329 \n", "Abnormality of the upper limb [HP:0002817] 0.696329 \n", - "Abnormality of limbs [HP:0040064] 0.696329 \n", - "Abnormal external nose morphology [HP:0010938] 0.705301 \n", - "Abnormal nasal morphology [HP:0005105] 0.705301 \n", "Abnormality of the nose [HP:0000366] 0.705301 \n", + "Abnormal nasal morphology [HP:0005105] 0.705301 \n", + "Abnormal external nose morphology [HP:0010938] 0.705301 \n", "Abnormal lip morphology [HP:0000159] 0.711011 \n", - "Long philtrum [HP:0000343] 0.711011 \n", "Abnormal upper lip morphology [HP:0000177] 0.711011 \n", "Abnormality of the philtrum [HP:0000288] 0.711011 \n", - "Abnormal oral cavity morphology [HP:0000163] 1.000000 \n", - "Abnormality of the mouth [HP:0000153] 1.000000 \n", - "Abnormality of the dentition [HP:0000164] 1.000000 \n", - "Intellectual disability [HP:0001249] 1.000000 \n", - "Abnormality of the head [HP:0000234] 1.000000 \n", - "Abnormality of head or neck [HP:0000152] 1.000000 \n", "Triangular face [HP:0000325] 1.000000 \n", - "Abnormal facial shape [HP:0001999] 1.000000 \n", - "Abnormal dental morphology [HP:0006482] 1.000000 \n", - "Abnormality of the face [HP:0000271] 1.000000 \n", - "Macrodontia [HP:0001572] 1.000000 \n", - "Abnormal ear morphology [HP:0031703] 1.000000 \n", - "Phenotypic abnormality [HP:0000118] 1.000000 \n", - "Abnormality of the nervous system [HP:0000707] 1.000000 \n", - "Abnormal nervous system physiology [HP:0012638] 1.000000 \n", - "Neurodevelopmental abnormality [HP:0012759] 1.000000 \n", - "Abnormality of mental function [HP:0011446] 1.000000 \n", + "Abnormality of the mouth [HP:0000153] 1.000000 \n", "Abnormal oral morphology [HP:0031816] 1.000000 \n", + "Abnormal oral cavity morphology [HP:0000163] 1.000000 \n", "Abnormality of the orbital region [HP:0000315] 1.000000 \n", "Abnormality of the integument [HP:0001574] 1.000000 \n", "Abnormality of the ocular adnexa [HP:0032039] 1.000000 \n", "Abnormal skin adnexa morphology [HP:0011138] 1.000000 \n", "Abnormal ocular adnexa morphology [HP:0030669] 1.000000 \n", "Abnormal hair morphology [HP:0001595] 1.000000 \n", - "Neurodevelopmental delay [HP:0012758] 1.000000 \n", - "Global developmental delay [HP:0001263] 1.000000 \n", "All [HP:0000001] 1.000000 \n", + "Abnormality of the dentition [HP:0000164] 1.000000 \n", + "Phenotypic abnormality [HP:0000118] 1.000000 \n", + "Abnormality of the head [HP:0000234] 1.000000 \n", + "Abnormality of the face [HP:0000271] 1.000000 \n", + "Abnormality of the nervous system [HP:0000707] 1.000000 \n", + "Global developmental delay [HP:0001263] 1.000000 \n", + "Intellectual disability [HP:0001249] 1.000000 \n", + "Abnormality of mental function [HP:0011446] 1.000000 \n", + "Neurodevelopmental delay [HP:0012758] 1.000000 \n", + "Abnormal nervous system physiology [HP:0012638] 1.000000 \n", + "Macrodontia [HP:0001572] 1.000000 \n", "Atypical behavior [HP:0000708] 1.000000 \n", + "Abnormal dental morphology [HP:0006482] 1.000000 \n", + "Abnormal ear morphology [HP:0031703] 1.000000 \n", + "Abnormal facial shape [HP:0001999] 1.000000 \n", + "Abnormality of head or neck [HP:0000152] 1.000000 \n", + "Neurodevelopmental abnormality [HP:0012759] 1.000000 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G \n", " Corrected p value \n", @@ -2635,47 +2599,46 @@ "Abnormality of body height [HP:0000002] 1.0 \n", "Growth delay [HP:0001510] 1.0 \n", "Growth abnormality [HP:0001507] 1.0 \n", - "Hearing abnormality [HP:0000364] 1.0 \n", "Abnormal ear physiology [HP:0031704] 1.0 \n", + "Hearing abnormality [HP:0000364] 1.0 \n", "Abnormality of the ear [HP:0000598] 1.0 \n", + "Abnormality of limbs [HP:0040064] 1.0 \n", "Abnormality of the hand [HP:0001155] 1.0 \n", "Abnormality of the upper limb [HP:0002817] 1.0 \n", - "Abnormality of limbs [HP:0040064] 1.0 \n", - "Abnormal external nose morphology [HP:0010938] 1.0 \n", - "Abnormal nasal morphology [HP:0005105] 1.0 \n", "Abnormality of the nose [HP:0000366] 1.0 \n", + "Abnormal nasal morphology [HP:0005105] 1.0 \n", + "Abnormal external nose morphology [HP:0010938] 1.0 \n", "Abnormal lip morphology [HP:0000159] 1.0 \n", - "Long philtrum [HP:0000343] 1.0 \n", "Abnormal upper lip morphology [HP:0000177] 1.0 \n", "Abnormality of the philtrum [HP:0000288] 1.0 \n", - "Abnormal oral cavity morphology [HP:0000163] 1.0 \n", - "Abnormality of the mouth [HP:0000153] 1.0 \n", - "Abnormality of the dentition [HP:0000164] 1.0 \n", - "Intellectual disability [HP:0001249] 1.0 \n", - "Abnormality of the head [HP:0000234] 1.0 \n", - "Abnormality of head or neck [HP:0000152] 1.0 \n", "Triangular face [HP:0000325] 1.0 \n", - "Abnormal facial shape [HP:0001999] 1.0 \n", - "Abnormal dental morphology [HP:0006482] 1.0 \n", - "Abnormality of the face [HP:0000271] 1.0 \n", - "Macrodontia [HP:0001572] 1.0 \n", - "Abnormal ear morphology [HP:0031703] 1.0 \n", - "Phenotypic abnormality [HP:0000118] 1.0 \n", - "Abnormality of the nervous system [HP:0000707] 1.0 \n", - "Abnormal nervous system physiology [HP:0012638] 1.0 \n", - "Neurodevelopmental abnormality [HP:0012759] 1.0 \n", - "Abnormality of mental function [HP:0011446] 1.0 \n", + "Abnormality of the mouth [HP:0000153] 1.0 \n", "Abnormal oral morphology [HP:0031816] 1.0 \n", + "Abnormal oral cavity morphology [HP:0000163] 1.0 \n", "Abnormality of the orbital region [HP:0000315] 1.0 \n", "Abnormality of the integument [HP:0001574] 1.0 \n", "Abnormality of the ocular adnexa [HP:0032039] 1.0 \n", "Abnormal skin adnexa morphology [HP:0011138] 1.0 \n", "Abnormal ocular adnexa morphology [HP:0030669] 1.0 \n", "Abnormal hair morphology [HP:0001595] 1.0 \n", - "Neurodevelopmental delay [HP:0012758] 1.0 \n", - "Global developmental delay [HP:0001263] 1.0 \n", "All [HP:0000001] 1.0 \n", - "Atypical behavior [HP:0000708] 1.0 " + "Abnormality of the dentition [HP:0000164] 1.0 \n", + "Phenotypic abnormality [HP:0000118] 1.0 \n", + "Abnormality of the head [HP:0000234] 1.0 \n", + "Abnormality of the face [HP:0000271] 1.0 \n", + "Abnormality of the nervous system [HP:0000707] 1.0 \n", + "Global developmental delay [HP:0001263] 1.0 \n", + "Intellectual disability [HP:0001249] 1.0 \n", + "Abnormality of mental function [HP:0011446] 1.0 \n", + "Neurodevelopmental delay [HP:0012758] 1.0 \n", + "Abnormal nervous system physiology [HP:0012638] 1.0 \n", + "Macrodontia [HP:0001572] 1.0 \n", + "Atypical behavior [HP:0000708] 1.0 \n", + "Abnormal dental morphology [HP:0006482] 1.0 \n", + "Abnormal ear morphology [HP:0031703] 1.0 \n", + "Abnormal facial shape [HP:0001999] 1.0 \n", + "Abnormality of head or neck [HP:0000152] 1.0 \n", + "Neurodevelopmental abnormality [HP:0012759] 1.0 " ] }, "execution_count": 19, diff --git a/src/genophenocorr/preprocessing/_phenopacket.py b/src/genophenocorr/preprocessing/_phenopacket.py index 57ca2de7..da03c3cf 100644 --- a/src/genophenocorr/preprocessing/_phenopacket.py +++ b/src/genophenocorr/preprocessing/_phenopacket.py @@ -50,6 +50,9 @@ def find_coordinates(self, item: GenomicInterpretation) -> typing.Tuple[VariantC vc = None if self._vcf_is_available(variant_descriptor.vcf_record): # We have a VCF record. + if not self._check_assembly(variant_descriptor.vcf_record.genome_assembly): + raise ValueError(f"Variant id {variant_descriptor.id} for patient {item.subject_or_biosample_id} has a different Genome Assembly than what was given. " \ + + f"{variant_descriptor.vcf_record.genome_assembly} is not {self._build.identifier}.") contig = self._build.contig_by_name(variant_descriptor.vcf_record.chrom) start = int(variant_descriptor.vcf_record.pos) - 1 ref = variant_descriptor.vcf_record.ref @@ -93,6 +96,15 @@ def find_coordinates(self, item: GenomicInterpretation) -> typing.Tuple[VariantC return vc, gt + def _check_assembly(self, genome_assembly:str) -> bool: + if '38' in genome_assembly and self._build.identifier == 'GRCh38.p13': + return True + elif ('37' in genome_assembly or '19' in genome_assembly) and self._build.identifier == 'GRCh37.p13': + return True + else: + return False + + @staticmethod def _vcf_is_available(vcf_record) -> bool: """ @@ -152,13 +164,7 @@ def create_patient(self, item: Phenopacket) -> Patient: """ sample_id = self._extract_id(item) phenotypes = self._add_phenotypes(item) - if len(phenotypes) == 0: - self._logger.warning('Patient %s has no phenotypes listed and will not be included in this analysis.', sample_id) - return None variants = self._add_variants(sample_id, item) - if len(variants) == 0: - self._logger.warning('Patient %s has no variants listed and will not be included in this analysis.', sample_id) - return None protein_data = self._add_protein_data(variants) return Patient(item.id, phenotypes, variants, protein_data) @@ -216,7 +222,10 @@ def _add_phenotypes(self, pp: Phenopacket) -> typing.Sequence[Phenotype]: if len(hpo_id_list) == 0: self._logger.warning(f'Expected at least one HPO term per patient, but received none for patient {pp.id}') return [] - return self._phenotype_creator.create_phenotype(hpo_id_list) + phenotypes, ignored_phenotypes = self._phenotype_creator.create_phenotype(hpo_id_list) + if len(ignored_phenotypes) != 0: + self._logger.warning("Patient %s had %i unknown phenotypes: %s", pp.id, len(ignored_phenotypes), ', '.join(ignored_phenotypes)) + return phenotypes def _add_protein_data(self, variants: typing.Sequence[Variant]) -> typing.Collection[ProteinMetadata]: """Creates a list of ProteinMetadata objects from a given list of Variant objects @@ -236,6 +245,7 @@ def _add_protein_data(self, variants: typing.Sequence[Variant]) -> typing.Collec def load_phenopacket_folder(pp_directory: str, patient_creator: PhenopacketPatientCreator, + #policy:str = "strict/lenient/etc", include_patients_with_no_HPO: bool = False) -> Cohort: """ Creates a Patient object for each phenopacket formatted JSON file in the given directory `pp_directory`. @@ -245,6 +255,7 @@ def load_phenopacket_folder(pp_directory: str, :param patient_creator: patient creator for turning a phenopacket into a :class:`genophenocorr.Patient` :return: a cohort made of the phenopackets """ + ## NOTE: Strict would stop code at error vs lenient would just print error but continue. if not os.path.isdir(pp_directory): raise ValueError("Could not find directory of Phenopackets.") hpotk.util.validate_instance(patient_creator, PhenopacketPatientCreator, 'patient_creator') @@ -258,6 +269,10 @@ def load_phenopacket_folder(pp_directory: str, patients = [] for pp in tqdm(pps, desc='Patients Created'): patient = patient_creator.create_patient(pp) + if len(patient.phenotypes) == 0: + patient_creator._logger.warning('Patient %s has no phenotypes listed and will not be included in this analysis.', patient.patient_id) + if len(patient.variants) == 0: + patient_creator._logger.warning('Patient %s has no variants listed and will not be included in this analysis.', patient.patient_id) if patient is not None: patients.append(patient) @@ -283,3 +298,4 @@ def load_phenopacket(phenopacket_path: str) -> Phenopacket: """ with open(phenopacket_path) as f: return Parse(f.read(), Phenopacket()) + diff --git a/src/genophenocorr/preprocessing/_phenotype.py b/src/genophenocorr/preprocessing/_phenotype.py index cb226e54..f5d1b631 100644 --- a/src/genophenocorr/preprocessing/_phenotype.py +++ b/src/genophenocorr/preprocessing/_phenotype.py @@ -34,7 +34,7 @@ def __init__(self, hpo: hpotk.MinimalOntology, self._hpo = hpotk.util.validate_instance(hpo, hpotk.MinimalOntology, 'hpo') self._validator = hpotk.util.validate_instance(validator, hpotk.validate.ValidationRunner, 'validator') - def create_phenotype(self, term_ids: typing.Iterable[typing.Tuple[str, bool]]) -> typing.Sequence[Phenotype]: + def create_phenotype(self, term_ids: typing.Iterable[typing.Tuple[str, bool]]) -> typing.Tuple[typing.Sequence[Phenotype], typing.Sequence[str]]: """Creates a list of Phenotype objects from term IDs and checks if the term IDs satisfy the validation requirements. Args: @@ -45,15 +45,17 @@ def create_phenotype(self, term_ids: typing.Iterable[typing.Tuple[str, bool]]) - PhenotypeValidationException: An instance of an issue with the ValidationRunner """ terms = [] + ignored_terms = [] for term_id, observed in term_ids: term = self._hpo.get_term(term_id) if term is None: self._logger.warning("Term %s cannot be found in HPO version %s. It will be ignored.", term_id, self._hpo.version) + ignored_terms.append(term_id) else: terms.append((term, observed)) validation_results = self._validator.validate_all([term[0] for term in terms]) if validation_results.is_ok: - return tuple(Phenotype.from_term(term, observed) for term, observed in terms) + return tuple(Phenotype.from_term(term, observed) for term, observed in terms), ignored_terms else: # We return the messages for now. We may provide more details in future, if necessary. issues = [r.message for r in validation_results.results] From 9e7e15a06b8f3e70fb5c6863ea68df0be331f17c Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 9 Jan 2024 14:55:40 -0500 Subject: [PATCH 02/25] Add auditors. --- src/genophenocorr/preprocessing/_audit.py | 90 +++++++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 src/genophenocorr/preprocessing/_audit.py diff --git a/src/genophenocorr/preprocessing/_audit.py b/src/genophenocorr/preprocessing/_audit.py new file mode 100644 index 00000000..9382d873 --- /dev/null +++ b/src/genophenocorr/preprocessing/_audit.py @@ -0,0 +1,90 @@ +import abc +import enum +import typing + + +class Level(enum.Enum): + """ + An enum to represent severity of the :class:`DataSanityIssue`. + """ + + WARN = enum.auto() + """ + Warning is an issue when something not entirely right. However, unlike :class:`Level.ERROR`, the analysis should + complete albeit with sub-optimal results 😧. + """ + + ERROR = enum.auto() + """ + Error is a serious issue in the input data and the downstream analysis may not complete or the analysis results + may be malarkey 😱. + """ + + +class DataSanityIssue: + """ + `DataSanityIssue` summarizes an issue found in the input data. + + The issue has a `level`, a `message` with human-friendly description, and the proposed `solution` + for removing the issue. + """ + + def __init__(self, level, message, solution): + self._level = level + self._message = message + self._solution = solution + + @property + def level(self) -> Level: + return self._level + + @property + def message(self) -> str: + return self._message + + @property + def solution(self) -> str: + return self._solution + + +IN = typing.TypeVar('IN') +""" +:class:`Auditor` input. +""" + +OUT = typing.TypeVar('OUT') +""" +:class:`Auditor` output format. +""" + + +class AuditReport(typing.Generic[OUT]): + """ + `AuditReport` includes the issues found by :class:`Auditor` and the outcome of the sanitation. + """ + + def __init__(self, outcome: OUT, + issues: typing.Iterable[DataSanityIssue]): + self._outcome = outcome + self._issues = tuple(issues) + + @property + def outcome(self) -> OUT: + return self._outcome + + @property + def issues(self) -> typing.Sequence[DataSanityIssue]: + return self._issues + + +class Auditor(typing.Generic[IN, OUT], metaclass=abc.ABCMeta): + """ + `Auditor` checks the inputs for sanity issues and relates the issues with sanitized inputs + as :class:`SanitationResults`. + + The input sanitation is optional so getting unsanitized input is permitted. + """ + + @abc.abstractmethod + def sanitize(self, inputs: IN) -> AuditReport[OUT]: + pass From b696a33a86b320da72d9d05d9984331810036993 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 9 Jan 2024 16:29:48 -0500 Subject: [PATCH 03/25] Use `SampleLabels` to represent sample ID instead of a simple `str`. --- src/genophenocorr/data/_toy.py | 52 ++++++++-------- src/genophenocorr/model/__init__.py | 4 +- src/genophenocorr/model/_base.py | 60 +++++++++++++++++++ src/genophenocorr/model/_cohort.py | 20 +++++-- src/genophenocorr/model/_gt.py | 39 +++++++----- .../preprocessing/_phenopacket.py | 19 +++--- tests/fixtures.py | 24 ++++---- 7 files changed, 147 insertions(+), 71 deletions(-) create mode 100644 src/genophenocorr/model/_base.py diff --git a/src/genophenocorr/data/_toy.py b/src/genophenocorr/data/_toy.py index 7a918c1a..76c90e35 100644 --- a/src/genophenocorr/data/_toy.py +++ b/src/genophenocorr/data/_toy.py @@ -77,132 +77,132 @@ def get_toy_cohort() -> Cohort: Genotypes.empty()) # Not used in the patients below, hence `empty()`. patients = ( - Patient('A', + Patient(SampleLabels('A'), phenotypes=(arachnodactyly_T, spasticity_F, seizure_T), variants=[snv], proteins=[prot] ), - Patient('B', + Patient(SampleLabels('B'), phenotypes=(arachnodactyly_T, seizure_T, spasticity_T), variants=[snv], proteins=[prot] ), - Patient('C', + Patient(SampleLabels('C'), phenotypes=(arachnodactyly_F, spasticity_T, seizure_T), variants=[snv], proteins=[prot] ), - Patient('D', + Patient(SampleLabels('D'), phenotypes=(arachnodactyly_T, spasticity_T, seizure_T), variants=[snv, deletion], proteins=[prot] ), - Patient('E', + Patient(SampleLabels('E'), phenotypes=(arachnodactyly_T, spasticity_T, seizure_F), variants=[snv], proteins=[prot] ), - Patient('F', + Patient(SampleLabels('F'), phenotypes=(arachnodactyly_F, spasticity_F, seizure_T), variants=[deletion], proteins=[prot] ), - Patient('G', + Patient(SampleLabels('G'), phenotypes=(arachnodactyly_T, seizure_T, spasticity_T), variants=[snv, deletion], proteins=[prot] ), - Patient('H', + Patient(SampleLabels('H'), phenotypes=(arachnodactyly_T, seizure_T, spasticity_F), variants=[deletion], proteins=[prot] ), - Patient('I', + Patient(SampleLabels('I'), phenotypes=(arachnodactyly_F, spasticity_F, seizure_T), variants=[deletion], proteins=[prot] ), - Patient('J', + Patient(SampleLabels('J'), phenotypes=(arachnodactyly_T, seizure_T, spasticity_T), variants=[snv], proteins=[prot] ), - Patient('K', + Patient(SampleLabels('K'), phenotypes=(arachnodactyly_F, spasticity_T, seizure_T), variants=[snv], proteins=[prot] ), - Patient('L', + Patient(SampleLabels('L'), phenotypes=(arachnodactyly_F, seizure_F, spasticity_F), variants=[deletion], proteins=[prot] ), - Patient('M', + Patient(SampleLabels('M'), phenotypes=(arachnodactyly_T, seizure_F, spasticity_T), variants=[snv], proteins=[prot] ), - Patient('N', + Patient(SampleLabels('N'), phenotypes=(arachnodactyly_F, seizure_T, spasticity_F), variants=[snv], proteins=[prot] ), - Patient('O', + Patient(SampleLabels('O'), phenotypes=(arachnodactyly_F, seizure_F, spasticity_T), variants=[deletion], proteins=[prot] ), - Patient('P', + Patient(SampleLabels('P'), phenotypes=(arachnodactyly_T, seizure_T, spasticity_F), variants=[snv], proteins=[prot] ), - Patient('Q', + Patient(SampleLabels('Q'), phenotypes=(arachnodactyly_T, seizure_F, spasticity_F), variants=[snv], proteins=[prot] ), - Patient('R', + Patient(SampleLabels('R'), phenotypes=(arachnodactyly_T, seizure_T, spasticity_F), variants=[snv, deletion], proteins=[prot] ), - Patient('S', + Patient(SampleLabels('S'), phenotypes=(arachnodactyly_F, seizure_T, spasticity_T), variants=[deletion], proteins=[prot] ), - Patient('T', + Patient(SampleLabels('T'), phenotypes=(arachnodactyly_T, seizure_F, spasticity_T), variants=[snv], proteins=[prot] ), - Patient('U', + Patient(SampleLabels('U'), phenotypes=(arachnodactyly_F, seizure_T, spasticity_T), variants=[deletion], proteins=[prot] ), - Patient('V', + Patient(SampleLabels('V'), phenotypes=(arachnodactyly_T, seizure_T, spasticity_T), variants=[snv], proteins=[prot] ), - Patient('W', + Patient(SampleLabels('W'), phenotypes=(arachnodactyly_F, seizure_T, spasticity_T), variants=[deletion], proteins=[prot] ), - Patient('X', + Patient(SampleLabels('X'), phenotypes=(arachnodactyly_F, seizure_T, spasticity_T), variants=[deletion], proteins=[prot] ), - Patient('Y', + Patient(SampleLabels('Y'), phenotypes=(arachnodactyly_T, seizure_T, spasticity_T), variants=[snv], proteins=[prot] ), - Patient('Z', + Patient(SampleLabels('Z'), phenotypes=(arachnodactyly_F, seizure_T, spasticity_T), variants=[deletion], proteins=[prot] diff --git a/src/genophenocorr/model/__init__.py b/src/genophenocorr/model/__init__.py index 6144a942..c6c2568a 100644 --- a/src/genophenocorr/model/__init__.py +++ b/src/genophenocorr/model/__init__.py @@ -4,7 +4,7 @@ and protein info. """ from . import genome - +from ._base import SampleLabels from ._cohort import Cohort, Patient from ._gt import Genotype, Genotypes, Genotyped from ._phenotype import Phenotype @@ -14,7 +14,7 @@ from ._variant_effects import VariantEffect __all__ = [ - 'Cohort', 'Patient', + 'Cohort', 'Patient', 'SampleLabels', 'Phenotype', 'Variant', 'VariantCoordinates', 'Genotype', 'Genotypes', 'Genotyped', 'TranscriptAnnotation', 'VariantEffect', 'TranscriptInfoAware', 'TranscriptCoordinates', diff --git a/src/genophenocorr/model/_base.py b/src/genophenocorr/model/_base.py new file mode 100644 index 00000000..36716831 --- /dev/null +++ b/src/genophenocorr/model/_base.py @@ -0,0 +1,60 @@ +import typing + +import hpotk + + +class SampleLabels: + """ + A data model for subject identifiers. + + The subject has a mandatory :attr:`label` and an optional :attr:`meta_label`. + + The identifiers support natural ordering, equality tests, and are hashable. + """ + + def __init__(self, label: str, + meta_label: typing.Optional[str] = None): + self._label = hpotk.util.validate_instance(label, str, 'label') + self._meta_label = hpotk.util.validate_optional_instance(meta_label, str, 'meta_label') + + @property + def label(self) -> str: + return self._label + + @property + def meta_label(self) -> typing.Optional[str]: + return self._meta_label + + def label_summary(self) -> str: + """ + Summarize `label` and `meta_label` into a `str` where the sub-parts are inserted as ``