Entity Name Entity type Gene Symbol Sources(; separated) Level4 Level3 Level2 Model_Of_Inheritance Phenotypes Omim Orphanet HPO Publications Description Flagged GEL_Status UserRatings_Green_amber_red version ready Mode of pathogenicity EnsemblId(GRch37) EnsemblId(GRch38) HGNC Position Chromosome Position GRCh37 Start Position GRCh37 End Position GRCh38 Start Position GRCh38 End STR Repeated Sequence STR Normal Repeats STR Pathogenic Repeats Region Haploinsufficiency Score Region Triplosensitivity Score Region Required Overlap Percentage Region Variant Type Region Verbose Name CDH11 gene CDH11 Expert Review Green;Literature Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Elsahy-Waters syndrome 27431290;29271567 False 3 100;0;0 0.483 True ENSG00000140937 ENSG00000140937 HGNC:1750 CLCN4 gene CLCN4 Expert Review Green Intellectual disability update Jan 2018 X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) "Mental retardation, X-linked 49/15 300114" 25644381 False 3 0;0;0 0.483 True ENSG00000073464 ENSG00000073464 HGNC:2022 CLTC gene CLTC Expert Review Green;Gene2Phenotype Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown "Mental retardation, autosomal dominant 56, 617854;Autosomal dominant non-syndromic intellectual disability;Epilepsy and intellectual disability" 26822784;29100083 False 3 0;0;0 0.483 True ENSG00000141367 ENSG00000141367 HGNC:2092 COG5 gene COG5 Expert Review Green Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted "Congenital disorder of glycosylation, type IIi 613612" 19690088;23430875;23228021;28960046 False 3 0;0;0 0.483 True ENSG00000164597 ENSG00000164597 HGNC:14857 GABRG2 gene GABRG2 BRIDGE study SPEED NEURO Tier1 Gene;Expert Review Green Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown "Epilepsy, generalized, with febrile seizures plus, type 3 611277;Febrile seizures, familial, 8 611277;{Epilepsy, childhood absence, susceptibility to, 2} 607681" 25124326;28460589 False 3 0;0;0 0.483 True ENSG00000113327 ENSG00000113327 HGNC:4087 GFER gene GFER Expert Review Green;Radboud University Medical Center, Nijmegen Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Myopathy, mitochondrial progressive, with congenital cataract, hearing loss, and developmental delay, 613076;Intellectual disability 19409522;26018198;28155230 False 3 100;0;0 0.483 True ENSG00000127554 ENSG00000127554 HGNC:4236 GMPPB gene GMPPB Expert Review Green;Radboud University Medical Center, Nijmegen Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 615350;Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 615351;Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 615352" 23768512;26503795;24896178 False 3 0;0;0 0.483 True ENSG00000173540 ENSG00000173540 HGNC:22932 GPAA1 gene GPAA1 Expert Review Green;Other Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal "Glycosylphosphatidylinositol biosynthesis defect 15 617810" 29100095;24896178 False 3 0;0;0 0.483 True ENSG00000197858 ENSG00000197858 HGNC:4446 GRID2 gene GRID2 BRIDGE study SPEED NEURO Tier1 Gene;Expert Review Green Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Spinocerebellar ataxia, autosomal recessive 18 616204 28856174;24078737;23611888;7792064;20395510 False 3 0;0;0 0.483 True ENSG00000152208 ENSG00000152208 HGNC:4576 HIVEP2 gene HIVEP2 Expert Review Green Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Mental retardation, autosomal dominant 43, 616977;MRD43;Intellectual disability 23020937;26153216;27003583;26350204 False 3 0;0;0 0.483 True ENSG00000010818 ENSG00000010818 HGNC:4921 KIAA1109 gene KIAA1109 Expert Review Green;Literature Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Brain atrophy, Dandy Walker and Contractures 25558065;29290337 False 3 100;0;0 0.483 True ENSG00000138688 ENSG00000138688 HGNC:26953 KMT2C gene KMT2C Expert Review Green Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Kleefstra syndrome 2 617768 22726846;29069077;29276005 False 3 0;0;0 0.483 True ENSG00000055609 ENSG00000055609 HGNC:13726 LARGE1 gene LARGE1 Expert Review Green;Gene2Phenotype Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 6, 613154;Muscle-eye-brain disease;MDDGA6;Walker-Warburg syndrome;Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 6, 608840;congenital muscular dystrophy-dystroglycanopathy with mental retardation;MDDGB6;Intellectual disability 12966029;19067344;17436019;19299310;21248746 False 3 0;0;0 0.483 True ENSG00000133424 ENSG00000133424 HGNC:6511 LONP1 gene LONP1 Expert Review Green Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal CODAS syndrome, 600373;Cerebral, ocular, dental, auricular, and skeletal anomalies syndrome 25574826;20503327 False 3 0;0;0 0.483 True ENSG00000196365 ENSG00000196365 HGNC:9479 MBOAT7 gene MBOAT7 Expert Review Green;Gene2Phenotype Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 57, 617188;Intellectual Disability Accompanied by Epilepsy and Autistic Features;Autosomal recessive non-syndromic intellectual disability 27616480;23097495 False 3 0;0;0 0.483 True ENSG00000125505 ENSG00000125505 HGNC:15505 MBTPS2 gene MBTPS2 Emory Genetics Laboratory;Expert Review Green;Radboud University Medical Center, Nijmegen Intellectual disability update Jan 2018 X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) IFAP syndrome with or without BRESHECK syndrome,308205;Ichthyosis follicularis, atrichia, and photophobia with or without brain anomalies, retardation, ectodermal dysplasia, skeletal malformations, hirschsprung disease, ear/eye anomalies, cleft palate/cryptorchidism, and kidney dysplasia/hypoplasia 21426410;22105905;24090718;23316014;21179107;19361614 False 3 0;0;0 0.483 True ENSG00000012174 ENSG00000012174 HGNC:15455 MDH2 gene MDH2 BRIDGE study SPEED NEURO Tier1 Gene;Expert Review Green Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal "Epileptic encephalopathy, early infantile, 51 617339" 27989324 False 3 0;0;0 0.483 True ENSG00000146701 ENSG00000146701 HGNC:6971 MTOR gene MTOR Expert Review Green Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Smith-Kingsmore syndrome, 616638;Intellectual Disability;Focal cortical dysplasia, type II, somatic 607341 26542245;27830187;25851998;28892148;DOI: 10.4137/JGE.S12583;27159400 False 3 100;0;0 0.483 True Other - please provide details in the comments ENSG00000198793 ENSG00000198793 HGNC:3942 NDST1 gene NDST1 Expert Review Green Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 46, 616116;MRT46;Intellectual disability 25125150;21937992 False 3 0;0;0 0.483 True Other - please provide details in the comments ENSG00000070614 ENSG00000070614 HGNC:7680 NFIA gene NFIA Expert Review Green Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Brain malformations with or without urinary tract defects, 613735;BRMUTD;Intellectual disability;Chromosome 1p32-p31 deletion syndrome, included 24462883;27081522;25714559;22031302;17530927 False 3 0;0;0 0.483 True ENSG00000162599 ENSG00000162599 HGNC:7784 NONO gene NONO BRIDGE study SPEED NEURO Tier1 Gene;Expert Review Green Intellectual disability update Jan 2018 X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Mental retardation, X-linked, syndromic 34, 300967;MENTAL RETARDATION, X-LINKED, SYNDROMIC, MIRCSOF-LANGOUET TYPE;MRXSML;Macrocephaly-intellectual disability-left ventricular non compaction syndrome;Syndromic intellectual disability 26571461;27329731;27329731;27550220 False 3 0;0;0 0.483 True ENSG00000147140 ENSG00000147140 HGNC:7871 NT5C2 gene NT5C2 BRIDGE study SPEED NEURO Tier1 Gene;Expert Review Green Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 45, autosomal recessive, 613162;Intellectual disability 20301682;24482476;19415352 False 3 0;0;0 0.483 True ENSG00000076685 ENSG00000076685 HGNC:8022 CLCN2 gene CLCN2 BRIDGE study SPEED NEURO Tier1 Gene;Expert Review Amber Intellectual disability update Jan 2018 BOTH monoallelic and biallelic, autosomal or pseudoautosomal Leukoencephalopathy with ataxia, 615651;{Epilepsy, juvenile myoclonic, susceptibility to, 8}, 607628;{Epilepsy, juvenile absence, susceptibility to, 2}, 607628;{Epilepsy, idiopathic generalized, susceptibility to, 11}, 607628 23707145;19191339 False 2 0;0;0 0.483 True ENSG00000114859 ENSG00000114859 HGNC:2020 GBA2 gene GBA2 Expert Review Amber Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal "Spastic paraplegia 46, autosomal recessive 614409" 23332916;23332917;24252062;28052128 False 2 0;0;0 0.483 True ENSG00000070610 ENSG00000070610 HGNC:18986 GJB1 gene GJB1 Expert Review Amber;Radboud University Medical Center, Nijmegen Intellectual disability update Jan 2018 X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) "Charcot-Marie-Tooth neuropathy, X-linked dominant, 1 302800" 26503795;23279342;26385972 False 2 0;0;0 0.483 True ENSG00000169562 ENSG00000169562 HGNC:4283 GRIA1 gene GRIA1 Expert Review Amber Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Intellectual disability 28628100;23033978;26350204;24896178 False 2 0;0;0 0.483 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000155511 ENSG00000155511 HGNC:4571 GSS gene GSS Expert Review Amber;Radboud University Medical Center, Nijmegen Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal "Glutathione synthetase deficiency 266130;Hemolytic anemia due to glutathione synthetase deficiency 231900" 29340523;24896178;26503795;8896573;15990954 False 2 0;0;0 0.483 True ENSG00000100983 ENSG00000100983 HGNC:4624 HAX1 gene HAX1 Expert Review Amber;Radboud University Medical Center, Nijmegen Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal "Neutropenia, severe congenital 3, autosomal recessive 610738" 18611981;24896178;26503795 False 2 0;0;0 0.483 True ENSG00000143575 ENSG00000143575 HGNC:16915 HIST1H4C gene HIST1H4C Expert Review Amber;Gene2Phenotype Intellectual disability update Jan 2018 Growth delay, microcephaly and intellectual disability 28920961 False 2 0;0;0 0.483 True ENSG00000197061 ENSG00000197061 HGNC:4787 KLHL15 gene KLHL15 Expert Review Amber Intellectual disability update Jan 2018 X-LINKED: hemizygous mutation in males, biallelic mutations in females Mental retardation, X-linked 103, 300982;MRX103;Intellectual disability 26350204;24817631;25644381 False 2 0;0;0 0.483 True ENSG00000174010 ENSG00000174010 HGNC:29347 KMT2B gene KMT2B BRIDGE study SPEED NEURO Tier1 Gene;Expert Review Amber Intellectual disability update Jan 2018 "Dystonia 28, childhood-onset 617284" 27839873;27992417;29276005;25405613;29289525 False 2 0;0;0 0.483 True ENSG00000272333 ENSG00000272333 HGNC:15840 MAPK10 gene MAPK10 Expert Review Amber Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Lennox-Gastaut syndrome;LGS;Epileptic Encephalopathy;Epileptic Encephalopathy Lennox-Gastaut type 23329067 False 2 0;100;0 0.483 True ENSG00000109339 ENSG00000109339 HGNC:6872 MED23 gene MED23 Expert Review Amber;Radboud University Medical Center, Nijmegen Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 18, 614249;MRT18;Intellectual disability 21868677;25845469;25527630;22129135 False 2 0;0;0 0.483 True ENSG00000112282 ENSG00000112282 HGNC:2372 MED25 gene MED25 Expert Review Amber;Literature Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Basel-Vanagait-Smirin-Yosef syndrome, 616449;BVSYS;Syndromic intellectual disability;Congenital cataract-microcephaly-nevus flammeus simplex-severe intellectual disability syndrome 25792360;25527630 False 2 0;0;0 0.483 True ENSG00000104973 ENSG00000104973 HGNC:28845 MIR17HG gene MIR17HG Expert Review Amber Intellectual disability update Jan 2018 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Feingold syndrome 2, 614326;FS2;Brachydactyly with short stature and microcephaly;Intellectual disability 21892160;19344873;25391829;26360630 False 2 0;0;0 0.483 True ENSG00000215417 ENSG00000215417 HGNC:23564 NDUFAF2 gene NDUFAF2 Expert Review Amber Intellectual disability update Jan 2018 BIALLELIC, autosomal or pseudoautosomal Leigh syndrome 256000;Mitochondrial complex I deficiency 252010 16200211;20818383;20571988 False 2 0;0;0 0.483 True ENSG00000164182 ENSG00000164182 HGNC:28086