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 ABAT gene ABAT Expert Review Red;Literature Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal GABA-transaminase deficiency Tsuji et al (2010) A new case of GABA transaminase deficiency facilitated by proton MR spectroscopy. J Inherit Metab Dis 33(1):85-90 False 1 100;0;0 1.158 False ENSG00000183044 ENSG00000183044 HGNC:23 ALDH7A1 gene ALDH7A1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000164904 ENSG00000164904 HGNC:877 AP3B2 gene AP3B2 Literature Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Epileptic encephalopathy, early infantile, 48 617276" 27889060 False 1 100;0;0 1.158 False ENSG00000103723 ENSG00000103723 HGNC:567 ATP1A2 gene ATP1A2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000018625 ENSG00000018625 HGNC:800 BTD gene BTD Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000169814 ENSG00000169814 HGNC:1122 CACNA1A gene CACNA1A Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000141837 ENSG00000141837 HGNC:1388 CACNA1H gene CACNA1H Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000196557 ENSG00000196557 HGNC:1395 CACNB4 gene CACNB4 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000182389 ENSG00000182389 HGNC:1404 CASK gene CASK Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000147044 ENSG00000147044 HGNC:1497 CBL gene CBL Expert Review;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders Martin et al (2014) Hum Mol Genet 23(12).3200-3211 False 1 0;0;100 1.158 False ENSG00000110395 ENSG00000110395 HGNC:1541 CCDC88C gene CCDC88C Literature Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal ?Spinocerebellar ataxia 40 616053 AD;Hydrocephalus, nonsyndromic, autosomal recessive 236600 AR 23042809;21031079 False 1 100;0;0 1.158 False ENSG00000015133 ENSG00000015133 HGNC:19967 CHRNA2 gene CHRNA2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Epilepsy, nocturnal frontal lobe, type 4 Aridon et al (2006) Am J Hum Genet 79: 342-350 False 1 75;0;25 1.158 True ENSG00000120903 ENSG00000120903 HGNC:1956 CHRNA4 gene CHRNA4 Expert;Expert Review Red;UKGTN Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Epilepsy, nocturnal frontal lobe, 1 Steinlein et al (1995) Nature Genet 11: 201-203 False 1 75;0;25 1.158 True ENSG00000101204 ENSG00000101204 HGNC:1958 CHRNB2 gene CHRNB2 Expert;Expert Review Red;UKGTN Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Epilepsy, nocturnal frontal lobe, 3 De Fusco et al (2001) Nature Genet 26: 275-276 False 1 75;0;25 1.158 True ENSG00000160716 ENSG00000160716 HGNC:1962 CLN3 gene CLN3 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000188603 ENSG00000188603 HGNC:2074 CLN5 gene CLN5 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000102805 ENSG00000102805 HGNC:2076 CLN6 gene CLN6 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000128973 ENSG00000128973 HGNC:2077 CLN8 gene CLN8 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000182372 ENSG00000182372 HGNC:2079 COL4A1 gene COL4A1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000187498 ENSG00000187498 HGNC:2202 COL4A2 gene COL4A2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000134871 ENSG00000134871 HGNC:2203 CRH gene CRH Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000147571 ENSG00000147571 HGNC:2355 CSNK1G1 gene CSNK1G1 Expert Review;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders Martin et al (2014) Hum Mol Genet 23(12).3200-3211 False 1 0;0;100 1.158 False ENSG00000169118 ENSG00000169118 HGNC:2454 CSTB gene CSTB Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False Other - please provide details in the comments ENSG00000160213 ENSG00000160213 HGNC:2482 CTSD gene CTSD Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000117984 ENSG00000117984 HGNC:2529 DEPDC5 gene DEPDC5 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000100150 ENSG00000100150 HGNC:18423 EEF1A2 gene EEF1A2 Expert Review Red;Radboud University Medical Center, Nijmegen Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000101210 ENSG00000101210 HGNC:3192 EFHC1 gene EFHC1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000096093 ENSG00000096093 HGNC:16406 EPM2A gene EPM2A Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000112425 ENSG00000112425 HGNC:3413 GABRD gene GABRD Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000187730 ENSG00000187730 HGNC:4084 GABRG2 gene GABRG2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000113327 ENSG00000113327 HGNC:4087 GAMT gene GAMT Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000130005 ENSG00000130005 HGNC:4136 GATAD2B gene GATAD2B Expert Review;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders Willemsen et al (2013) J Med Genet 50:507 514 False 1 0;0;100 1.158 False ENSG00000143614 ENSG00000143614 HGNC:30778 GATM gene GATM Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000171766 ENSG00000171766 HGNC:4175 GLRA1 gene GLRA1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000145888 ENSG00000145888 HGNC:4326 GLRB gene GLRB Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000109738 ENSG00000109738 HGNC:4329 GOSR2 gene GOSR2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000108433 ENSG00000108433 HGNC:4431 GPHN gene GPHN Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000171723 ENSG00000171723 HGNC:15465 HLCS gene HLCS Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000159267 ENSG00000159267 HGNC:4976 KCNA1 gene KCNA1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000111262 ENSG00000111262 HGNC:6218 KCNC1 gene KCNC1 Expert Review;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders Muona et al (2015) Nat Genet 47(1): 39-46 False 1 0;0;100 1.158 False ENSG00000129159 ENSG00000129159 HGNC:6233 KCNMA1 gene KCNMA1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000156113 ENSG00000156113 HGNC:6284 KCTD7 gene KCTD7 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000243335 ENSG00000243335 HGNC:21957 LGI1 gene LGI1 Expert;Expert Review Red;UKGTN Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Epilepsy, familial temporal lobe, 1 Berkovic et al (2004) Neurology 62: 1115-1119 False 1 75;0;25 1.158 True ENSG00000108231 ENSG00000108231 HGNC:6572 MAGI2 gene MAGI2 Expert Review Red;UKGTN Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Infantile Spasms Marshall et al (2008) Am J Hum Genet 83: 106_111 False 1 80;0;20 1.158 True ENSG00000187391 ENSG00000187391 HGNC:18957 MFSD8 gene MFSD8 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000164073 ENSG00000164073 HGNC:28486 MOCS1 gene MOCS1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000124615 ENSG00000124615 HGNC:7190 MOCS2 gene MOCS2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000164172 ENSG00000164172 HGNC:7193 MT-TL1 gene MT-TL1 Expert Review Red;UKGTN Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders MITOCHONDRIAL False 1 0;0;100 1.158 False ENSG00000209082 ENSG00000209082 HGNC:7490 NECAP1 gene NECAP1 Expert Review Red;Radboud University Medical Center, Nijmegen Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders ?Epileptic encephalopathy, early infantile,21 False 1 0;0;100 1.158 False ENSG00000089818 ENSG00000089818 HGNC:24539 NHLRC1 gene NHLRC1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000187566 ENSG00000187566 HGNC:21576 NRXN1 gene NRXN1 Expert;Expert Review Red;UKGTN Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal False 1 0;0;100 1.158 False ENSG00000179915 ENSG00000179915 HGNC:8008 PCDH12 gene PCDH12 Expert Review Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal intellectual disability;microcephaly;epilepsy;perithalamic hyperechogenicity;periventricular hyperechogenicity;midbrain abnormalities;hypothalamic abnormalities 27164683 False 1 0;0;100 1.158 False ENSG00000113555 ENSG00000113555 HGNC:8657 PIGQ gene PIGQ Expert Review;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders Martin et al (2014) Hum Mol Genet 23(12).3200-3211 False 1 0;20;80 1.158 False ENSG00000007541 ENSG00000007541 HGNC:14135 PNPO gene PNPO Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders 24658933;28818555;22196487;21704546;25296925;26535729;15772097;24266778;24658933 False 1 20;0;80 1.158 False ENSG00000108439 ENSG00000108439 HGNC:30260 PPT1 gene PPT1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000131238 ENSG00000131238 HGNC:9325 PRICKLE1 gene PRICKLE1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000139174 ENSG00000139174 HGNC:17019 PRICKLE2 gene PRICKLE2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000163637 ENSG00000163637 HGNC:20340 RYR3 gene RYR3 Expert Review;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders EuroEPINOMICS-RES Consortium (2014) AJHG 95:1-11 False 1 0;0;100 1.158 False ENSG00000198838 ENSG00000198838 HGNC:10485 SCARB2 gene SCARB2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000138760 ENSG00000138760 HGNC:1665 SCN2B gene SCN2B Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000149575 ENSG00000149575 HGNC:10589 SCN9A gene SCN9A Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000169432 ENSG00000169432 HGNC:10597 SLC6A5 gene SLC6A5 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000165970 ENSG00000165970 HGNC:11051 SLC6A8 gene SLC6A8 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000130821 ENSG00000130821 HGNC:11055 SMS gene SMS Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000102172 ENSG00000102172 HGNC:11123 SRPX2 gene SRPX2 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000102359 ENSG00000102359 HGNC:30668 ST3GAL3 gene ST3GAL3 Expert Review Red;Radboud University Medical Center, Nijmegen Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders Epileptic encephalopathy, early infantile, 15 False 1 0;0;100 1.158 False ENSG00000126091 ENSG00000126091 HGNC:10866 TBC1D24 gene TBC1D24 Expert;Expert Review Red;Radboud University Medical Center, Nijmegen;UKGTN Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal False 1 0;0;100 1.158 False ENSG00000162065 ENSG00000162065 HGNC:29203 TBL1XR1 gene TBL1XR1 Expert Review;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000177565 ENSG00000177565 HGNC:29529 TPP1 gene TPP1 Expert;Expert Review Red Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders False 1 0;0;100 1.158 False ENSG00000166340 ENSG00000166340 HGNC:2073 TSC2 gene TSC2 Expert Review Red;Literature Epileptic encephalopathy Inherited Epilepsy Syndromes Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Focal cortical dysplasia, type II, somatic 607341 28215400;19175396 False 1 0;0;0 1.158 False Other - please provide details in the comments ENSG00000103197 ENSG00000103197 HGNC:12363