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 AHI1 gene AHI1 Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Joubert syndrome 3, MIM# 608629 Abnormal cerebral cortex morphology;HP:0002538 15467982 False 2 0;100;0 4.69 True ENSG00000135541 ENSG00000135541 HGNC:21575 ASTN1 gene ASTN1 Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Polymicrogyria;hypoplastic corpus callosum Abnormal cerebral cortex morphology;HP:0002538 29706646 False 2 0;100;0 4.69 True ENSG00000152092 ENSG00000152092 HGNC:773 BRAF gene BRAF Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted RASopathies;Focal cortical dysplasia Abnormal cerebral cortex morphology;HP:0002538 18039946;18039235;25356392 False 2 0;100;0 4.69 True ENSG00000157764 ENSG00000157764 HGNC:1097 CDK5 gene CDK5 Expert Review Amber;Expert list Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Lissencephaly 7 with cerebellar hypoplasia, MIM# 616342" Abnormal cerebral cortex morphology;HP:0002538 25560765;32273484;32097629;28854363;7490100 False 2 0;100;0 4.69 True ENSG00000164885 ENSG00000164885 HGNC:1774 COL4A2 gene COL4A2 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Brain small vessel disease 2, MIM#614483 Abnormal cerebral cortex morphology;HP:0002538 30315939 False 2 0;100;0 4.69 True ENSG00000134871 ENSG00000134871 HGNC:2203 CSNK2A1 gene CSNK2A1 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown "Okur-Chung neurodevelopmental syndrome (MIM#617062)" Abnormal cerebral cortex morphology;HP:0002538 27048600;29240241 False 2 0;100;0 4.69 True ENSG00000101266 ENSG00000101266 HGNC:2457 EMX2 gene EMX2 Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Schizencephaly MIM# 269160 Abnormal cerebral cortex morphology;HP:0002538 8528262;9359037;9153481;18409201 False 2 0;100;0 4.69 True ENSG00000170370 ENSG00000170370 HGNC:3341 FAT4 gene FAT4 Expert Review Amber;Australian Genomics Health Alliance Brain Malformation Flagship;Victorian Clinical Genetics Services Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Van Maldergem syndrome 2, MIM# 615546 Abnormal cerebral cortex morphology;HP:0002538 22473091;24056717 False 2 0;100;0 4.69 True ENSG00000196159 ENSG00000196159 HGNC:23109 FIG4 gene FIG4 Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Polymicrogyria with epilepsy MIM# 612691 Abnormal cerebral cortex morphology;HP:0002538 18758830;24598713 False 2 0;100;0 4.69 True ENSG00000112367 ENSG00000112367 HGNC:16873 GMPPB gene GMPPB Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 (MIM# 615350);Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 14 (MIM# 615351);Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 (MIM# 615352) Abnormal cerebral cortex morphology;HP:0002538 23768512;30257713;26310427;24780531 False 2 0;100;0 4.69 True ENSG00000173540 ENSG00000173540 HGNC:22932 KAT6B gene KAT6B Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted SBBYSS syndrome MIM #603736;Genitopatellar syndrome MIM #606170 Abnormal cerebral cortex morphology;HP:0002538 32424177;23236640 False 2 0;100;0 4.69 True ENSG00000156650 ENSG00000156650 HGNC:17582 L1CAM gene L1CAM Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders X-LINKED: hemizygous mutation in males, biallelic mutations in females L1CAM-related disease Abnormal cerebral cortex morphology;HP:0002538 9926316;27066571 False 2 0;100;0 4.69 True ENSG00000198910 ENSG00000198910 HGNC:6470 MED25 gene MED25 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Basel-Vanagait-Smirin-Yosef syndrome, MIM# 616449 Abnormal cerebral cortex morphology;HP:0002538 32324310;32816121 False 2 0;100;0 4.69 True ENSG00000104973 ENSG00000104973 HGNC:28845 MFN2 gene MFN2 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Mitochondrial disease, MONDO:0044970, MFN2-related Abnormal cerebral cortex morphology;HP:0002538 PMID: 37804319 False 2 0;100;0 4.69 True ENSG00000116688 ENSG00000116688 HGNC:16877 MFN2 gene MFN2 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Mitochondrial disease, MONDO:0044970, MFN2-related Abnormal cerebral cortex morphology;HP:0002538 PMID: 37804319 False 2 0;100;0 4.69 True ENSG00000116688 ENSG00000116688 HGNC:16877 NHEJ1 gene NHEJ1 Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders Unknown Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation (MIM# 611291) Abnormal cerebral cortex morphology;HP:0002538 17191205 False 2 0;100;0 4.69 True ENSG00000187736 ENSG00000187736 HGNC:25737 NSDHL gene NSDHL Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders X-LINKED: hemizygous mutation in males, biallelic mutations in females CK syndrome 300831 Abnormal cerebral cortex morphology;HP:0002538 19377476;19842190;21129721 False 2 0;100;0 4.69 True ENSG00000147383 ENSG00000147383 HGNC:13398 NSDHL gene NSDHL Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders X-LINKED: hemizygous mutation in males, biallelic mutations in females CK syndrome 300831 Abnormal cerebral cortex morphology;HP:0002538 19377476;19842190;21129721 False 2 0;100;0 4.69 True ENSG00000147383 ENSG00000147383 HGNC:13398 PAX6 gene PAX6 Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted ?Coloboma of optic nerve MIM# 120430;?Coloboma, ocular MIM# 120200;?Morning glory disc anomaly MIM# 120430;Aniridia MIM# 106210;Anterior segment dysgenesis 5, multiple subtypes MIM# 604229;Cataract with late-onset corneal dystrophy MIM# 106210;Foveal hypoplasia 1 MIM# 136520;Keratitis MIM# 148190;Optic nerve hypoplasia MIM# 165550 Abnormal cerebral cortex morphology;HP:0002538 12731001 False 2 0;100;0 4.69 True ENSG00000007372 ENSG00000007372 HGNC:8620 PEX10 gene PEX10 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Peroxisome biogenesis disorder 6A (Zellweger) (MIM#614870)" Abnormal cerebral cortex morphology;HP:0002538 21031596 False 2 0;100;0 4.69 True ENSG00000157911 ENSG00000157911 HGNC:8851 PEX12 gene PEX12 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Peroxisome biogenesis disorder 3A (Zellweger) (MIM#614859)" Abnormal cerebral cortex morphology;HP:0002538 21031596 False 2 0;100;0 4.69 True ENSG00000108733 ENSG00000108733 HGNC:8854 PEX13 gene PEX13 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Peroxisome biogenesis disorder 11A (Zellweger) (MIM#614883)" Abnormal cerebral cortex morphology;HP:0002538 21031596;19449432 False 2 0;100;0 4.69 True ENSG00000162928 ENSG00000162928 HGNC:8855 PEX14 gene PEX14 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Peroxisome biogenesis disorder 8A (Zellweger) MIM#614876 Abnormal cerebral cortex morphology;HP:0002538 21031596;18285423;15146459;30224891 False 2 0;100;0 4.69 True ENSG00000142655 ENSG00000142655 HGNC:8856 PEX16 gene PEX16 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Peroxisome biogenesis disorder 8A (Zellweger) MIM#614876 Abnormal cerebral cortex morphology;HP:0002538 21031596 False 2 0;100;0 4.69 True ENSG00000121680 ENSG00000121680 HGNC:8857 PEX19 gene PEX19 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Peroxisome biogenesis disorder 12A (Zellweger) MIM#614886 Abnormal cerebral cortex morphology;HP:0002538 21031596 False 2 0;100;0 4.69 True ENSG00000162735 ENSG00000162735 HGNC:9713 PEX2 gene PEX2 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Peroxisome biogenesis disorder 5A (Zellweger) MIM#614866 Abnormal cerebral cortex morphology;HP:0002538 21031596 False 2 0;100;0 4.69 True ENSG00000164751 ENSG00000164751 HGNC:9717 PEX26 gene PEX26 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Peroxisome biogenesis disorder 7A (Zellweger) MIM#614872 Abnormal cerebral cortex morphology;HP:0002538 21031596 False 2 0;100;0 4.69 True ENSG00000215193 ENSG00000215193 HGNC:22965 PEX3 gene PEX3 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Peroxisome biogenesis disorder 10A (Zellweger) 614882" Abnormal cerebral cortex morphology;HP:0002538 21031596 False 2 0;100;0 4.69 True ENSG00000034693 ENSG00000034693 HGNC:8858 PEX5 gene PEX5 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Peroxisome biogenesis disorder 2A (Zellweger) (MIM#214110) Abnormal cerebral cortex morphology;HP:0002538 21031596 False 2 0;100;0 4.69 True ENSG00000139197 ENSG00000139197 HGNC:9719 PI4KA gene PI4KA Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, MIM# 616531 Abnormal cerebral cortex morphology;HP:0002538 25855803;34415322 False 2 0;100;0 4.69 True ENSG00000241973 ENSG00000241973 HGNC:8983 SMO gene SMO Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders Unknown Curry-Jones syndrome, somatic mosaic MIM#601707 Abnormal cerebral cortex morphology;HP:0002538 27236920;24859340 False 2 0;100;0 4.69 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000128602 ENSG00000128602 HGNC:11119 STRADA gene STRADA Expert Review Amber;Victorian Clinical Genetics Services;Australian Genomics Health Alliance Brain Malformations Flagship Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Polyhydramnios, megalencephaly, and symptomatic epilepsy (MIM#611087) Abnormal cerebral cortex morphology;HP:0002538 28688840;17522105;27170158;23616120 False 2 100;0;0 4.69 True ENSG00000266173 ENSG00000266173 HGNC:30172 TMX2 gene TMX2 Expert Review Amber;Literature Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with microcephaly, cortical malformations, and spasticity MIM#618730 Abnormal cerebral cortex morphology;HP:0002538 31735293;31586943 False 2 0;100;0 4.69 True ENSG00000213593 ENSG00000213593 HGNC:30739 TTL gene TTL Expert Review Amber;Other Malformations of cortical development_Superpanel Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal complex neurodevelopmental disorder MONDO:0100038 Abnormal cerebral cortex morphology;HP:0002538 False 2 0;100;0 4.69 True ENSG00000114999 ENSG00000114999 HGNC:21586