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 ACTB gene ACTB Expert Review Green;Emory Genetics Laboratory;UKGTN;Radboud University Medical Center, Nijmegen;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Baraitser Winter syndrome (lissencephaly, pachygyria, polymicrogyria, ptosis, coloboma) False 3 100;0;0 15.65 True ENSG00000075624 ENSG00000075624 HGNC:132 ACTG1 gene ACTG1 Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Emory Genetics Laboratory;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Baraitser Winter Syndrome False 3 100;0;0 15.65 True ENSG00000184009 ENSG00000184009 HGNC:144 ADGRG1 gene ADGRG1 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;UKGTN Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal "Polymicrogyria, bilateral frontoparietal 606854;Polymicrogyria, bilateral perisylvian 615752" False 3 100;0;0 15.65 True ENSG00000205336 ENSG00000205336 HGNC:4512 AKT1 gene AKT1 Expert Review Green Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Proteus syndrome, somatic, OMIM:176920;Macrocephaly and Overgrowth Syndromes;Segmental Overgrowth Syndrome;Proteus syndrome 33030203 False 3 100;0;0 15.65 False ENSG00000142208 ENSG00000142208 HGNC:391 AKT3 gene AKT3 Expert Review Green Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937;Macrocephaly and Overgrowth Syndromes False 3 100;0;0 15.65 False ENSG00000117020 ENSG00000117020 HGNC:393 AKT3 gene AKT3 Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937 False 3 100;0;0 15.65 True ENSG00000117020 ENSG00000117020 HGNC:393 APC2 gene APC2 Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Cortical dysplasia, complex, with other brain malformations 10 OMIM:618677 31585108;25753423;19759310;22573669 False 3 100;0;0 15.65 False ENSG00000115266 ENSG00000115266 HGNC:24036 ARF1 gene ARF1 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Periventricular nodular heterotopia 8, OMIM:618185 28868155;34353862 False 3 100;0;0 15.65 False ENSG00000143761 ENSG00000143761 HGNC:652 ARFGEF2 gene ARFGEF2 Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Emory Genetics Laboratory;Illumina TruGenome Clinical Sequencing Services;Expert Review Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Periventricular nodular heterotopia False 3 100;0;0 15.65 True ENSG00000124198 ENSG00000124198 HGNC:15853 ARX gene ARX Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Lissencephaly, X-Linked, 2 300215;Epileptic encephalopathy, early infantile, 1 308350;Hydranencephaly with abnormal genitalia 300215;Mental retardation, X-linked 29 and others 300419;Partington syndrome 309510;Proud syndrome 300004 False 3 100;0;0 15.65 True ENSG00000004848 ENSG00000004848 HGNC:18060 ASPM gene ASPM Expert Review Green;UKGTN;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly 5, primary, autosomal recessive, OMIM:608716 12355089;14574646;16673149;18452193;19028728;19353628;19770472;22775483;27250695;30500859 False 3 100;0;0 15.65 True ENSG00000066279 ENSG00000066279 HGNC:19048 ATP1A2 gene ATP1A2 Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic facies, OMIM:619602 30690204;31608932 False 3 100;0;0 15.65 False ENSG00000018625 ENSG00000018625 HGNC:800 ATP1A3 gene ATP1A3 NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Polymicrogyria, MONDO:0000087;epilepsy, MONDO:0005027;developmental delay;Developmental and epileptic encephalopathy 99, OMIM:619606 33762331;33880529 False 3 100;0;0 15.65 False ENSG00000105409 ENSG00000105409 HGNC:801 B3GALNT2 gene B3GALNT2 Expert Review Green;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies, type A, 11 615181 23453667 False 3 100;0;0 15.65 True ENSG00000162885 ENSG00000162885 HGNC:28596 B4GAT1 gene B4GAT1 NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13, OMIM:615287 23359570;23877401;23217742 False 3 67;0;33 15.65 True ENSG00000174684 ENSG00000174684 HGNC:15685 CASK gene CASK Expert Review Green;NHS GMS Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Mental retardation and microcephaly with pontine and cerebellar hypoplasia OMIM:300749 21954287;20595373;32700313;33090494;33272775;35149592 False 3 100;0;0 15.65 False ENSG00000147044 ENSG00000147044 HGNC:1497 CASP2 gene CASP2 Expert Review Green;NHS GMS;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly, OMIM:620653 37880421 False 3 100;0;0 15.65 False ENSG00000106144 ENSG00000106144 HGNC:1503 CCND2 gene CCND2 Expert Review Green Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3, OMIM:615938 False 3 100;0;0 15.65 False ENSG00000118971 ENSG00000118971 HGNC:1583 CCND2 gene CCND2 Expert Review Green;UKGTN;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3 615938 24705253, 27854409 False 3 100;0;0 15.65 True Other - please provide details in the comments ENSG00000118971 ENSG00000118971 HGNC:1583 CDH2 gene CDH2 Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Agenesis of corpus callosum, cardiac, ocular, and genital syndrome, OMIM:618929;Agenesis of corpus callosum, cardiac, ocular, and genital syndrome, MONDO:0030065 31585109;31650526 False 3 100;0;0 15.65 False ENSG00000170558 ENSG00000170558 HGNC:1759 CDK13 gene CDK13 Expert Review Green;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Congenital heart defects, dysmorphic facial features, and intellectual development disorder 617360 27479907;25529582 False 3 67;0;33 15.65 False ENSG00000065883 ENSG00000065883 HGNC:1733 CDK5 gene CDK5 NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Lissencephaly 7 with cerebellar hypoplasia, OMIM:616342;lissencephaly 7 with cerebellar hypoplasia, MONDO:0014596 25560765;40186457;28854363;8855328 False 3 100;0;0 15.65 False ENSG00000164885 ENSG00000164885 HGNC:1774 CDON gene CDON NHS GMS;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 11, 614226;Holoprosencephaly 21802063 False 3 0;100;0 15.65 False ENSG00000064309 ENSG00000064309 HGNC:17104 CEP85L gene CEP85L Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Lissencephaly 10, OMIM:618873;Lissencephaly 10, MONDO:0030031 32097630;32097629 False 3 100;0;0 15.65 False ENSG00000111860 ENSG00000111860 HGNC:21638 CNOT1 gene CNOT1 Expert Review Green;NHS GMS;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 12, with or without pancreatic agenesis, OMIM:618500;holoprosencephaly 12 with or without pancreatic agenesis, MONDO:0032787 31006513;31006510;35481434 False 3 100;0;0 15.65 False Other ENSG00000125107 ENSG00000125107 HGNC:7877 COL3A1 gene COL3A1 Expert Review Green;NHS GMS;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Polymicrogyria with or without vascular-type EDS, OMIM:618343;polymicrogyria with or without vascular-type Ehlers-Danlos syndrome, MONDO:0032688 19455184;25205403;28742248;28258187 False 3 100;0;0 15.65 False ENSG00000168542 ENSG00000168542 HGNC:2201 COL4A1 gene COL4A1 Expert Review Green;NHS GMS;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, OMIM:611773;Brain small vessel disease with or without ocular anomalies, OMIM:175780;Microangiopathy and leukoencephalopathy, pontine, autosomal dominant, OMIM:618564;{Hemorrhage, intracerebral, susceptibility to}, OMIM:614519 30837194;37157232;30413629;36324412 False 3 100;0;0 15.65 False ENSG00000187498 ENSG00000187498 HGNC:2202 COL4A2 gene COL4A2 Expert Review Green;NHS GMS;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Brain small vessel disease 2, OMIM:614483;{Hemorrhage, intracerebral, susceptibility to}, OMIM:614519 30413629;36324412;22333902 False 3 100;0;0 15.65 False ENSG00000134871 ENSG00000134871 HGNC:2203 CRADD gene CRADD Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 34, with variant lissencephaly, OMIM:614499 22279524;27773430;30914828 False 3 100;0;0 15.65 False ENSG00000169372 ENSG00000169372 HGNC:2340 CSNK2A1 gene CSNK2A1 Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Okur-Chung neurodevelopmental syndrome, OMIM:617062 27048600;29240241 False 3 50;50;0 15.65 False ENSG00000101266 ENSG00000101266 HGNC:2457 CTNNA2 gene CTNNA2 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Cortical dysplasia, complex, with other brain malformations 9, OMIM:618174 30013181 False 3 100;0;0 15.65 False ENSG00000066032 ENSG00000066032 HGNC:2510 DAG1 gene DAG1 Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Emory Genetics Laboratory Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 9 616538 24052401;25934851;12140559 False 3 33;0;67 15.65 True ENSG00000173402 ENSG00000173402 HGNC:2666 DCHS1 gene DCHS1 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Van Maldergem syndrome 1, OMIM:601390;Periventricular nodular heterotopia 22473091;24056717 False 3 100;0;0 15.65 False ENSG00000166341 ENSG00000166341 HGNC:13681 DCX gene DCX Expert Review Green;UKGTN;Emory Genetics Laboratory;Eligibility statement prior genetic testing;Other Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Lissencephaly, X-linked, OMIM:300067;Subcortical laminal heterotopia, X-linked, OMIM:300067 False 3 100;0;0 15.65 True ENSG00000077279 ENSG00000077279 HGNC:2714 DEPDC5 gene DEPDC5 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Epilepsy, familial focal, with variable foci 1, OMIM:604364;Focal cortical dysplasia 24585383;25623524;31444548;32848577;33949696;34055363;36067010 False 3 100;0;0 15.65 False ENSG00000100150 ENSG00000100150 HGNC:18423 DHCR7 gene DHCR7 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Smith-Lemli-Opitz syndrome, 270400;alobar holoprosencephaly (HPE) 11562938;28805615;20104611;17001700;15013448 False 3 0;100;0 15.65 False ENSG00000172893 ENSG00000172893 HGNC:2860 DISP1 gene DISP1 Expert Review Green;NHS GMS;Expert list Cerebral malformation Neurology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Holoprosencephaly 10, OMIM:621143;holoprosencephaly 10, MONDO:0976262 19184110;23542665;26748417;27363716;38529886 False 3 33;67;0 15.65 False ENSG00000154309 ENSG00000154309 HGNC:19711 DPYSL5 gene DPYSL5 NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder with corpus callosum agenesis and cerebellar abnormalities 33894126 False 3 100;0;0 15.65 False ENSG00000157851 ENSG00000157851 HGNC:20637 DYNC1H1 gene DYNC1H1 Expert Review Green;Radboud University Medical Center, Nijmegen;Illumina TruGenome Clinical Sequencing Services;UKGTN;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Mental retardation, autosomal dominant 13 614563 False 3 100;0;0 15.65 True ENSG00000197102 ENSG00000197102 HGNC:2961 EML1 gene EML1 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Band heterotopia, OMIM:600348 24859200;28556411;31710781;34211111 False 3 100;0;0 15.65 False ENSG00000066629 ENSG00000066629 HGNC:3330 FGF8 gene FGF8 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Holoprosencephaly 27363716 False 3 0;100;0 15.65 False ENSG00000107831 ENSG00000107831 HGNC:3686 FGFR1 gene FGFR1 NHS GMS;Expert Review Green;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Hypogonadotropic hypogonadism 2 with or without anosmia, OMIM:147950;Hartsfield syndrome, OMIM:615465 19504604;27363716;23154428;23812909;25394172 False 3 67;33;0 15.65 False ENSG00000077782 ENSG00000077782 HGNC:3688 FKRP gene FKRP Expert Review Green;Radboud University Medical Center, Nijmegen;Emory Genetics Laboratory;UKGTN;Expert Review Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscle- eye- brain disease; Warburg syndrome False 3 100;0;0 15.65 True ENSG00000181027 ENSG00000181027 HGNC:17997 FKTN gene FKTN Expert Review Green;UKGTN;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen;Illumina TruGenome Clinical Sequencing Services Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4 253800 9690476 False 3 0;0;0 15.65 True Other - please provide details in the comments ENSG00000106692 ENSG00000106692 HGNC:3622 FLNA gene FLNA Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Heterotopia, periventricular, 1, OMIM:300049 False 3 100;0;0 15.65 True Other - please provide details in the comments ENSG00000196924 ENSG00000196924 HGNC:3754 GLI2 gene GLI2 NHS GMS;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-9;Holoprosencephaly;Holoprosencephaly 9, 610829 False 3 100;0;0 15.65 False ENSG00000074047 ENSG00000074047 HGNC:4318 GPSM2 gene GPSM2 Expert Review Green;UKGTN;Radboud University Medical Center, Nijmegen Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Chudley-McCullough syndrome 604213 20602914 False 3 100;0;0 15.65 True ENSG00000121957 ENSG00000121957 HGNC:29501 GRIN1 gene GRIN1 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254;intellectual disability, autosomal dominant 8 MONDO:0013655 29365063;33062288 False 3 100;0;0 15.65 False ENSG00000176884 ENSG00000176884 HGNC:4584 GRIN2B gene GRIN2B NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Intellectual developmental disorder, autosomal dominant 6, with or without seizures, OMIM:613970 28377535 False 3 100;0;0 15.65 False ENSG00000273079 ENSG00000273079 HGNC:4586 H3F3A gene H3F3A Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Developmental delay;Intellectual disability;Neurodegeneration;Epilepsy;Facial dysmorphism;Congenital anomalies 31942419;33268356 False 3 100;0;0 15.65 False ENSG00000163041 ENSG00000163041 HGNC:4764 HECTD4 gene HECTD4 Expert Review Green;NHS GMS;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with seizures, spasticity, and complete or partial agenesis of the corpus callosum, OMIM:620250 36401616 False 3 100;0;0 15.65 False ENSG00000173064 ENSG00000173064 HGNC:26611 ISPD gene ISPD Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN;Emory Genetics Laboratory Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7 614643 22522420 False 3 100;0;0 15.65 True ENSG00000214960 ENSG00000214960 HGNC:37276 KATNB1 gene KATNB1 Expert Review Green;Other Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Lissencephaly 6, with microcephaly, OMIM:616212, MONDO:0014534 25521379;25521378 False 3 0;0;0 15.65 True ENSG00000140854 ENSG00000140854 HGNC:6217 KIF1BP gene KIF1BP Expert Review Green;UKGTN;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;Emory Genetics Laboratory Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Goldberg-Shprintzen megacolon syndrome 609460 15883926 False 3 100;0;0 15.65 True ENSG00000198954 ENSG00000198954 HGNC:23419 KIF2A gene KIF2A Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Expert Review;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cortical dysplasia, complex, with other brain malformations 3 False 3 100;0;0 15.65 True ENSG00000068796 ENSG00000068796 HGNC:6318 KIF5C gene KIF5C Expert Review Green;Expert Review;UKGTN;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cortical dysplasia, complex, with other brain malformations 2 False 3 100;0;0 15.65 True ENSG00000168280 ENSG00000168280 HGNC:6325 KMT2D gene KMT2D Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Kabuki syndrome 1, OMIM:147920 31846209;31282990;32773771 False 3 100;0;0 15.65 False ENSG00000167548 ENSG00000167548 HGNC:7133 LAMA2 gene LAMA2 Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy, congenital, merosin deficient or partially deficient OMIM:607855 20207543;18406646;32827036 False 3 100;0;0 15.65 False ENSG00000196569 ENSG00000196569 HGNC:6482 LAMB1 gene LAMB1 Expert Review Green;UKGTN;Radboud University Medical Center, Nijmegen;Expert Review Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Lissencephaly 5 615191 False 3 100;0;0 15.65 True ENSG00000091136 ENSG00000091136 HGNC:6486 LAMC3 gene LAMC3 Expert Review Green;Emory Genetics Laboratory;UKGTN;Radboud University Medical Center, Nijmegen;Other Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Cortical malformations, occipital, OMIM:614115;occipital pachygyria and polymicrogyria, MONDO:0013583 21572413;26802095;29247375;33639934;34354730 False 3 100;0;0 15.65 True ENSG00000050555 ENSG00000050555 HGNC:6494 LARGE1 gene LARGE1 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;Emory Genetics Laboratory;UKGTN;Expert Review Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscle-eye-brain disease False 3 100;0;0 15.65 True ENSG00000133424 ENSG00000133424 HGNC:6511 MACF1 gene MACF1 Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Lissencephaly 9 with complex brainstem malformation, 618325 30471716 False 3 100;0;0 15.65 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000127603 ENSG00000127603 HGNC:13664 MAP1B gene MAP1B Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Periventricular nodular heterotopia 9, OMIM:618918 31317654;30150678;30214071 False 3 100;0;0 15.65 False ENSG00000131711 ENSG00000131711 HGNC:6836 MAPK8IP3 gene MAPK8IP3 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder with or without variable brain abnormalities, OMIM:618443 30612693;30945334 False 3 100;0;0 15.65 False ENSG00000138834 ENSG00000138834 HGNC:6884 MAX gene MAX Expert Review Green;NHS GMS;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Polydactyly-macrocephaly syndrome, OMIM:620712 38141607 False 3 100;0;0 15.65 False ENSG00000125952 ENSG00000125952 HGNC:6913 MN1 gene MN1 Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown CEBALID syndrome, OMIM:618774;CEBALID syndrome, MONDO:0032908 31834374;31839203;15870292 False 3 100;0;0 15.65 False ENSG00000169184 ENSG00000169184 HGNC:7180 MTOR gene MTOR Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Focal cortical dysplasia, type II, somatic 607341 26018084;27830187;25878179 False 3 0;0;0 15.65 False Other - please provide details in the comments ENSG00000198793 ENSG00000198793 HGNC:3942 NDE1 gene NDE1 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;UKGTN Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Lissencephaly 4 (with microcephaly) 614019;?Microhydranencephaly 605013 False 3 100;0;0 15.65 True ENSG00000072864 ENSG00000072864 HGNC:17619 NEDD4L gene NEDD4L Expert Review Green;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Periventricular nodular heterotopia 7 617201 27694961 False 3 100;0;0 15.65 True ENSG00000049759 ENSG00000049759 HGNC:7728 NFIA gene NFIA NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Brain malformations with or without urinary tract defects, OMIM:613735 27081522;28452798;33973697;36553517 False 3 100;0;0 15.65 False ENSG00000162599 ENSG00000162599 HGNC:7784 NPRL2 gene NPRL2 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Epilepsy, familial focal, with variable foci 2, OMIM:617116 29281825;27173016;31625153;30093711 False 3 50;50;0 15.65 False ENSG00000114388 ENSG00000114388 HGNC:24969 NPRL3 gene NPRL3 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Epilepsy, familial focal, with variable foci 3, OMIM:617118 27173016;26285051 False 3 100;0;0 15.65 False ENSG00000103148 ENSG00000103148 HGNC:14124 NSRP1 gene NSRP1 NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal NSRP1-associated developmental delay, epilepsy and microcephaly 34385670 False 3 100;0;0 15.65 False ENSG00000126653 ENSG00000126653 HGNC:25305 OCLN gene OCLN Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Band-like calcification with simplified gyration and polymicrogyria 251290 20727516 False 3 100;0;0 15.65 True ENSG00000197822 ENSG00000197822 HGNC:8104 OSGEP gene OSGEP Expert Review Green;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal "Galloway-Mowat syndrome 3 617729" 28805828 False 3 100;0;0 15.65 True ENSG00000092094 ENSG00000092094 HGNC:18028 PAFAH1B1 gene PAFAH1B1 Expert Review Green;Other;Illumina TruGenome Clinical Sequencing Services;UKGTN;Emory Genetics Laboratory;Eligibility statement prior genetic testing Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Lissencephaly 1, OMIM:607432;Subcortical laminar heterotopia, OMIM:607432 34635911 False 3 0;0;0 15.65 True ENSG00000007168 ENSG00000007168 HGNC:8574 PEX1 gene PEX1 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 1A (Zellweger), 214100;Peroxisome biogenesis disorder 1B (NALD/IRD), 601539 27604308 False 3 100;0;0 15.65 False ENSG00000127980 ENSG00000127980 HGNC:8850 PEX10 gene PEX10 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 6A (Zellweger), 614870;Peroxisome biogenesis disorder 6B, 614871 27604308 False 3 100;0;0 15.65 False ENSG00000157911 ENSG00000157911 HGNC:8851 PEX11B gene PEX11B Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Peroxisome biogenesis disorder 14B, 614920 False 3 100;0;0 15.65 False ENSG00000131779 ENSG00000131779 HGNC:8853 PEX12 gene PEX12 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 3A (Zellweger), 614859;Peroxisome biogenesis disorder 3B, 266510 27604308 False 3 100;0;0 15.65 False ENSG00000108733 ENSG00000108733 HGNC:8854 PEX13 gene PEX13 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 11A (Zellweger),614883 27604308 False 3 100;0;0 15.65 False ENSG00000162928 ENSG00000162928 HGNC:8855 PEX14 gene PEX14 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 13A (Zellweger), 614887 27604308 False 3 100;0;0 15.65 False ENSG00000142655 ENSG00000142655 HGNC:8856 PEX16 gene PEX16 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 8A, (Zellweger), 614876;Zellweger Syndrome;Peroxisome Biogenesis Disorders, Zellweger Syndrome Spectrum;Peroxisomal biogenesis disorders 27604308 False 3 100;0;0 15.65 False ENSG00000121680 ENSG00000121680 HGNC:8857 PEX19 gene PEX19 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 12A (Zellweger), 614886 27604308 False 3 100;0;0 15.65 False ENSG00000162735 ENSG00000162735 HGNC:9713 PEX2 gene PEX2 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 5A (Zellweger), 614866;Peroxisome biogenesis disorder 5B, 614867 27604308 False 3 100;0;0 15.65 False ENSG00000164751 ENSG00000164751 HGNC:9717 PEX26 gene PEX26 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 7A (Zellweger), 61487;Peroxisome biogenesis disorder 7B, 614873 27604308 False 3 100;0;0 15.65 False ENSG00000215193 ENSG00000215193 HGNC:22965 PEX3 gene PEX3 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 10A (Zellweger), 614882 27604308 False 3 100;0;0 15.65 False ENSG00000034693 ENSG00000034693 HGNC:8858 PEX5 gene PEX5 Literature;Expert Review Green Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Disorders of peroxisome biogenesis;Peroxisome biogenesis disorder 2A (Zellweger), 214110;Peroxisome biogenesis disorder 2B, 202370 27604308 False 3 100;0;0 15.65 False ENSG00000139197 ENSG00000139197 HGNC:9719 PEX6 gene PEX6 NHS GMS;Literature;Expert Review Green Cerebral malformation Neurology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Peroxisome biogenesis disorder 4A (Zellweger), OMIM:614862;Peroxisome biogenesis disorder 4B, OMIM:614863 27604308;29220678 False 3 100;0;0 15.65 False ENSG00000124587 ENSG00000124587 HGNC:8859 PI4KA gene PI4KA NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531 25855803;34415322;34415310 False 3 67;33;0 15.65 False ENSG00000241973 ENSG00000241973 HGNC:8983 PIDD1 gene PIDD1 NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Intellectual disability;Pachygyria;Lissencephaly;Seizures 33414379;34163010 False 3 100;0;0 15.65 False ENSG00000177595 ENSG00000177595 HGNC:16491 PIK3CA gene PIK3CA Expert Review Green Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cowden syndrome 5, OMIM:615108;CLAPO syndrome, somatic, OMIM:613089;CLOVE syndrome, somatic, OMIM:612918;Macrodactyly, somatic, OMIM:155500;Megalencephaly-capillary malformation-polymicrogyria syndrome, somatic, OMIM:602501 False 3 100;0;0 15.65 False ENSG00000121879 ENSG00000121879 HGNC:8975 PIK3CA gene PIK3CA Expert Review Green;UKGTN;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Polymicrogyria, hemimegalencephaly, macrocephaly False 3 100;0;0 15.65 True ENSG00000121879 ENSG00000121879 HGNC:8975 PIK3R2 gene PIK3R2 Expert Review Green;UKGTN;Radboud University Medical Center, Nijmegen;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1, OMIM:603387 False 3 100;0;0 15.65 True ENSG00000105647 ENSG00000105647 HGNC:8980 PIK3R2 gene PIK3R2 Expert Review Green Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1, OMIM:603387 False 3 100;0;0 15.65 False ENSG00000105647 ENSG00000105647 HGNC:8980 POMGNT1 gene POMGNT1 Expert Review Green;UKGTN;Illumina TruGenome Clinical Sequencing Services;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen;Expert Review Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3 253280 False 3 100;0;0 15.65 True ENSG00000085998 ENSG00000085998 HGNC:19139 POMGNT2 gene POMGNT2 Expert Review Green;UKGTN;Radboud University Medical Center, Nijmegen;Emory Genetics Laboratory Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies, type A, 8 614830 22958903 False 3 100;0;0 15.65 True ENSG00000144647 ENSG00000144647 HGNC:25902 POMT1 gene POMT1 Expert Review Green;UKGTN;Illumina TruGenome Clinical Sequencing Services;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen;Expert Review Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 1 236670;Type 2 lissencephaly False 3 100;0;0 15.65 True ENSG00000130714 ENSG00000130714 HGNC:9202 POMT2 gene POMT2 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen;UKGTN;Expert Review Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 2 613150;Type 2 lissencephaly False 3 100;0;0 15.65 True ENSG00000009830 ENSG00000009830 HGNC:19743 PPP1R12A gene PPP1R12A Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Genitourinary and/or/brain malformation syndrome, OMIM:618820 31883643 False 3 100;0;0 15.65 False ENSG00000058272 ENSG00000058272 HGNC:7618 PTCH1 gene PTCH1 NHS GMS;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;Other;UKGTN Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 7, OMIM:610828 False 3 100;0;0 15.65 False ENSG00000185920 ENSG00000185920 HGNC:9585 PTEN gene PTEN Expert Review Green Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cowden syndrome 1, OMIM:158350;Lhermitte-Duclos syndrome, OMIM:158350;Macrocephaly/autism syndrome, OMIM:605309 False 3 100;0;0 15.65 False ENSG00000171862 ENSG00000171862 HGNC:9588 PTEN gene PTEN NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cowden syndrome 1 OMIM:158350;Lhermitte-Duclos syndrome OMIM:158350;Cowden syndrome 1 MONDO:0008021;Macrocephaly/autism syndrome OMIM:605309;macrocephaly-autism syndrome MONDO:0011537 32162846 False 3 100;0;0 15.65 False ENSG00000171862 ENSG00000171862 HGNC:9588 RAB18 gene RAB18 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Warburg micro syndrome 3, OMIM:614222 21473985;23420520 False 3 100;0;0 15.65 False ENSG00000099246 ENSG00000099246 HGNC:14244 RAB3GAP1 gene RAB3GAP1 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Warburg micro syndrome 1 OMIM:600118;Warburg micro syndrome 1 MONDO:0010822 23420520;32740904;30730599;20512159 False 3 100;0;0 15.65 False ENSG00000115839 ENSG00000115839 HGNC:17063 RAB3GAP2 gene RAB3GAP2 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Warburg micro syndrome 2, OMIM:614225;Warburg micro syndrome 2 MONDO:0013641 23420520;20967465;32740904 False 3 100;0;0 15.65 False ENSG00000118873 ENSG00000118873 HGNC:17168 RAC3 gene RAC3 NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Neurodevelopmental disorder with structural brain anomalies and dysmorphic facies, OMIM:618577 29276006;30293988;35851598;35595279 False 3 100;0;0 15.65 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000169750 ENSG00000169750 HGNC:9803 RAD21 gene RAD21 Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cornelia de Lange syndrome 4, OMIM:614701;Holoprosencephaly with or without CdLS features;Septo-optic dysplasia 31334757;32696056 False 3 100;0;0 15.65 False ENSG00000164754 ENSG00000164754 HGNC:9811 RELN gene RELN Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Illumina TruGenome Clinical Sequencing Services;Emory Genetics Laboratory Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal "Lissencephaly 2 (Norman-Roberts type) 257320;Type 2 lissencephaly and cerebellar hypoplasia" 10973257;7682675 False 3 100;0;0 15.65 True ENSG00000189056 ENSG00000189056 HGNC:9957 RTTN gene RTTN Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Emory Genetics Laboratory Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly, short stature, and polymicrogyria with seizures 614833 26608784 False 3 100;0;0 15.65 True ENSG00000176225 ENSG00000176225 HGNC:18654 SCN3A gene SCN3A NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Polymicrogyria, MONDO:0000087;malformations of cortical development;epilepsy, MONDO:0005027;Developmental and epileptic encephalopathy 62, OMIM:617938 32515017;30146301;34081427 False 3 100;0;0 15.65 False ENSG00000153253 ENSG00000153253 HGNC:10590 SHH gene SHH NHS GMS;Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-3;Holoprosencephaly;Holoprosencephaly 3, 142945 False 3 100;0;0 15.65 False ENSG00000164690 ENSG00000164690 HGNC:10848 SIX3 gene SIX3 NHS GMS;Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-2;Holoprosencephaly;Holoprosencephaly 2, 157170 False 3 100;0;0 15.65 False ENSG00000138083 ENSG00000138083 HGNC:10889 SLC35A2 gene SLC35A2 NHS GMS;Expert Review Green;Literature Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE);Congenital disorder of glycosylation, type IIm, OMIM:300896 23561849;24115232;33407896 False 3 50;50;0 15.65 False ENSG00000102100 ENSG00000102100 HGNC:11022 SMC1A gene SMC1A Expert Review Green;Other Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Developmental and epileptic encephalopathy 85, with midline brain defects, OMIM:301044;Developmental and epileptic encephalopathy, 85, with or without midline brain defects, MONDO:0026771 28166369;31334757 False 3 100;0;0 15.65 False ENSG00000072501 ENSG00000072501 HGNC:11111 SMO gene SMO Expert Review Green;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Curry-Jones syndrome, somatic mosaic 601707 27236920 False 3 100;0;0 15.65 False ENSG00000128602 ENSG00000128602 HGNC:11119 SNAP29 gene SNAP29 Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome, OMIM:609528;CEDNIK syndrome, MONDO:0012290 15968592;21073448;25958742;28388629;29051910;30793783 False 3 100;0;0 15.65 False ENSG00000099940 ENSG00000099940 HGNC:11133 SOX11 gene SOX11 Expert Review Green;NHS GMS Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Coffin-Siris syndrome 9, OMIM:615866 24886874;26543203;23556151 False 3 100;0;0 15.65 False ENSG00000176887 ENSG00000176887 HGNC:11191 STAG2 gene STAG2 Expert Review Green;Other Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Holoprosencephaly 13, X-linked OMIM:301043 PMID: 31334757 False 3 100;0;0 15.65 False ENSG00000101972 ENSG00000101972 HGNC:11355 TBC1D32 gene TBC1D32 NHS GMS;Expert Review Green;Expert list;Radboud University Medical Center, Nijmegen Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Orofaciodigital syndrome IX, OMIM:258865;orofaciodigital syndrome IX, MONDO:0009795 32573025;31130284;32060556;24285566;35875813 False 3 100;0;0 15.65 False ENSG00000146350 ENSG00000146350 HGNC:21485 TGIF1 gene TGIF1 NHS GMS;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-4;Holoprosencephaly;Holoprosencephaly 4, 142946 False 3 100;0;0 15.65 False ENSG00000177426 ENSG00000177426 HGNC:11776 TMEM5 gene TMEM5 Expert Review Green;UKGTN;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 10 615041 23217329 False 3 100;0;0 15.65 True ENSG00000118600 ENSG00000118600 HGNC:13530 TMX2 gene TMX2 Expert Review Green;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with microcephaly, cortical malformations, and spasticity, OMIM:618730;Neurodevelopmental disorder with microcephaly, cortical malformations, and spasticity, MONDO:0032887 31586943;31735293;31270415 False 3 50;50;0 15.65 False ENSG00000213593 ENSG00000213593 HGNC:30739 TP73 gene TP73 NHS GMS;Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Ciliary dyskinesia, primary, 47, and lissencephaly, OMIM:619466 31130284;34077761 False 3 100;0;0 15.65 False ENSG00000078900 ENSG00000078900 HGNC:12003 TUBA1A gene TUBA1A Expert Review Green;Illumina TruGenome Clinical Sequencing Services;UKGTN Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Lissencephaly 3 611603 False 3 100;0;0 15.65 True ENSG00000167552 ENSG00000167552 HGNC:20766 TUBB gene TUBB Expert Review Green;UKGTN;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cortical dysplasia, complex, with other brain malformations 6, 615771 27010057;23246003;30016746 False 3 0;100;0 15.65 True ENSG00000196230 ENSG00000196230 HGNC:20778 TUBB2A gene TUBB2A Expert Review Green;UKGTN;Radboud University Medical Center, Nijmegen;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cortical dysplasia, complex, with other brain malformations 5, OMIM:615763;Complex cortical dysplasia with other brain malformations 5, MONDO:0014337 24702957;32571897 False 3 100;0;0 15.65 True ENSG00000137267 ENSG00000137267 HGNC:12412 TUBB2B gene TUBB2B Expert Review Green;Radboud University Medical Center, Nijmegen;Emory Genetics Laboratory;UKGTN Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cortical dysplasia, complex, with other brain malformations 7, OMIM:610031 False 3 100;0;0 15.65 True Other - please provide details in the comments ENSG00000137285 ENSG00000137285 HGNC:30829 TUBB3 gene TUBB3 Expert Review Green;UKGTN;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cortical dysplasia, complex, with other brain malformations 1 614039 20829227 False 3 0;0;0 15.65 True ENSG00000258947 ENSG00000258947 HGNC:20772 TUBG1 gene TUBG1 Expert Review Green;UKGTN;Radboud University Medical Center, Nijmegen;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cortical dysplasia, complex, with other brain malformations 4 615412 23603762;24860126;27010057;29706637;31151415 False 3 100;0;0 15.65 True ENSG00000131462 ENSG00000131462 HGNC:12417 TUBGCP2 gene TUBGCP2 Expert Review Green;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures, OMIM:618737 31630790 False 3 100;0;0 15.65 False ENSG00000130640 ENSG00000130640 HGNC:18599 VLDLR gene VLDLR Expert Review Green;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1 OMIM:224050 16080122;18364738;18326629;22700954;22973972 False 3 100;0;0 15.65 False ENSG00000147852 ENSG00000147852 HGNC:12698 WDR62 gene WDR62 Expert Review Green;UKGTN;Illumina TruGenome Clinical Sequencing Services;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen;Expert Review Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly 2, primary, autosomal recessive, with or without cortical malformations, OMIM:604317 21834044;20890278;20729831;28377545;10573015;20890279;30500859 False 3 100;0;0 15.65 True ENSG00000075702 ENSG00000075702 HGNC:24502 ZIC2 gene ZIC2 NHS GMS;Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly-5;Holoprosencephaly;Holoprosencephaly 5, 609637 False 3 100;0;0 15.65 False ENSG00000043355 ENSG00000043355 HGNC:12873 ASTN1 gene ASTN1 Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092 41544630 False 2 100;0;0 15.65 False ENSG00000152092 ENSG00000152092 HGNC:773 ATG12 gene ATG12 Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092;Hypoplasia of the corpus callosum, HP:0002079;Cerebellar hypoplasia, HP:0001321 41895291 False 2 100;0;0 15.65 False ENSG00000145782 ENSG00000145782 HGNC:588 CCT3 gene CCT3 Expert Review Amber;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder with speech or visual impairment and brain hypomyelination, OMIM:621034;neurodevelopmental disorder with speech or visual impairment and brain hypomyelination, MONDO:0976125 39480921 False 2 100;0;0 15.65 False ENSG00000163468 ENSG00000163468 HGNC:1616 CCT8 gene CCT8 Expert Review Amber;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted CCT8-related neurodevelopmental disorder with brain abnormalities 39480921 False 2 0;100;0 15.65 False ENSG00000156261 ENSG00000156261 HGNC:1623 CEP76 gene CEP76 Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal ciliopathy, MONDO:0005308;Joubert syndrome, MONDO:0018772;Bardet-Biedl syndrome, MONDO:0015229 41105778 False 2 100;0;0 15.65 False ENSG00000101624 ENSG00000101624 HGNC:25727 DLL1 gene DLL1 NHS GMS;Expert Review Amber;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 27363716;21196490;29771000 False 2 0;100;0 15.65 False ENSG00000198719 ENSG00000198719 HGNC:2908 EMX2 gene EMX2 Expert Review Amber;NHS GMS;Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Schizencephaly, OMIM:269160 8528262;9359037;18409201;17506092 False 2 25;75;0 15.65 False ENSG00000170370 ENSG00000170370 HGNC:3341 FAT4 gene FAT4 Expert Review Amber;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Van Maldergem syndrome 2, OMIM:615546 22473091;24056717 False 2 0;100;0 15.65 False ENSG00000196159 ENSG00000196159 HGNC:23109 FIG4 gene FIG4 Expert Review Amber;Expert list Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal ?Polymicrogyria, bilateral temporooccipital OMIM:612691;bilateral parasagittal parieto-occipital polymicrogyria MONDO:0012986 18758830;24598713 False 2 0;100;0 15.65 False ENSG00000112367 ENSG00000112367 HGNC:16873 FSD1L gene FSD1L Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092 41720098;41720099 False 2 100;0;0 15.65 False ENSG00000106701 ENSG00000106701 HGNC:13753 HS2ST1 gene HS2ST1 Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Intellectual disability;dysmorphic features;congenital anomalies 33159882 False 2 0;100;0 15.65 False ENSG00000153936 ENSG00000153936 HGNC:5193 JKAMP gene JKAMP Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092 41643666 False 2 100;0;0 15.65 False ENSG00000050130 ENSG00000050130 HGNC:20184 KIF26A gene KIF26A Expert Review Amber;Other Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Cortical dysplasia, complex, with other brain malformations 11, OMIM:620156;cortical dysplasia, complex, with other brain malformations 11 MONDO:0859332 36228617;36564622;39305096 False 2 100;0;0 15.65 False ENSG00000066735 ENSG00000066735 HGNC:20226 MYCBP2 gene MYCBP2 Expert Review Amber;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted neurodevelopmental disorder, MONDO:0700092 33875846;36200388;41200582;41543631 False 2 100;0;0 15.65 False ENSG00000005810 ENSG00000005810 HGNC:23386 PLCH1 gene PLCH1 Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Severe developmental delay;Brain malformations;Holoprosencephaly spectrum 33820834 False 2 0;100;0 15.65 False ENSG00000114805 ENSG00000114805 HGNC:29185 PPP1R12A gene PPP1R12A Expert Review Amber;Expert list Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Genitourinary and/or/brain malformation syndrome, 618820 31883643 False 2 50;50;0 15.65 False ENSG00000058272 ENSG00000058272 HGNC:7618 PPP2R1A gene PPP2R1A Expert Review Amber;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Houge-Janssens syndrome 2, OMIM:616362;Houge-Janssens syndrome 2, MONDO:0014605 33106617 False 2 100;0;0 15.65 False ENSG00000105568 ENSG00000105568 HGNC:9302 RDH11 gene RDH11 Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal ?Retinal dystrophy, juvenile cataracts, and short stature syndrome, OMIM:616108;Neurodevelopmental delay, HP:0012758;Juvenile cataract, HP:0001118 24916380;34988992;41459630;41904678 False 2 100;0;0 15.65 False ENSG00000072042 ENSG00000072042 HGNC:17964 SUFU gene SUFU NHS GMS;Expert Review Amber;Expert Review Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Basal cell nevus syndrome, OMIM:109400 27363716;29771000 False 2 0;100;0 15.65 False ENSG00000107882 ENSG00000107882 HGNC:16466 TCP1 gene TCP1 Expert Review Amber;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Intellectual developmental disorder with polymicrogyria and seizures, OMIM:621021;intellectual developmental disorder with polymicrogyria and seizures, MONDO:0976124 39480921 False 2 100;0;0 15.65 False ENSG00000120438 ENSG00000120438 HGNC:11655 TSC1 gene TSC1 Expert Review Amber;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Focal cortical dysplasia, type II, somatic 607341 28215400; 19175396; 16114042; 12112044 False 2 0;0;0 15.65 False Other - please provide details in the comments ENSG00000165699 ENSG00000165699 HGNC:12362 TUBA8 gene TUBA8 Expert Review Amber;Emory Genetics Laboratory;Radboud University Medical Center, Nijmegen;UKGTN Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Polymicrogyria with optic nerve hypoplasia 613180 19896110 False 2 100;0;0 15.65 True ENSG00000183785 ENSG00000183785 HGNC:12410 VPS50 gene VPS50 Expert Review Amber;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Neonatal cholestatic liver disease;Failure to thrive;Profound global developmental delay;Postnatal microcephaly;Seizures;Abnormality of the corpus callosum 34037727 False 2 0;100;0 15.65 False ENSG00000004766 ENSG00000004766 HGNC:25956 WNK3 gene WNK3 Expert Review Amber;Literature Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, biallelic mutations in females Prieto syndrome, OMIM:309610;Intellectual disability, MONDO:0001071 35678782 False 2 0;0;0 15.65 False ENSG00000196632 ENSG00000196632 HGNC:14543 ZNF865 gene ZNF865 Expert Review Amber;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted neurodevelopmental disorder, MONDO:0700092 40936200 False 2 100;0;0 15.65 False ENSG00000261221 ENSG00000261221 HGNC:38705 AKT2 gene AKT2 Expert Review Red Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Hypoinsulinemic hypoglycemia with hemihypertrophy, OMIM:240900;Hypoinsulinemic hypoglycemia and body hemihypertrophy, MONDO:0009416 False 1 0;0;0 15.65 False ENSG00000105221 ENSG00000105221 HGNC:392 BAIAP2 gene BAIAP2 Other Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown developmental and epileptic encephalopathy, MONDO:0100620;classic lissencephaly, MONDO:0015146 30696821;38149472;41133935 False 1 0;0;100 15.65 False ENSG00000175866 ENSG00000175866 HGNC:947 DLGAP4 gene DLGAP4 Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown 35585091 False 1 0;0;100 15.65 False ENSG00000080845 ENSG00000080845 HGNC:24476 ENO1 gene ENO1 Expert Review Red;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Polymicrogyria, MONDO:0000087 32488097 False 1 0;0;100 15.65 False ENSG00000074800 ENSG00000074800 HGNC:3350 EOMES gene EOMES Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal microcephaly syndrome 17353897 False 1 0;0;100 15.65 False ENSG00000163508 ENSG00000163508 HGNC:3372 ERMARD gene ERMARD Expert Review Red;UKGTN Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Periventricular nodular heterotopia 6 615544 24056535 False 1 0;0;100 15.65 True ENSG00000130023 ENSG00000130023 HGNC:21056 FOXH1 gene FOXH1 NHS GMS;Expert Review Red;Illumina TruGenome Clinical Sequencing Services Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 27363716 False 1 0;100;0 15.65 False ENSG00000160973 ENSG00000160973 HGNC:3814 GCM2 gene GCM2 NHS GMS;Expert Review Red;Other;UKGTN Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Hypoparathyroidism, familial isolated (AD) False 1 0;0;100 15.65 False ENSG00000124827 ENSG00000124827 HGNC:4198 GMPPB gene GMPPB Expert Review Red;Radboud University Medical Center, Nijmegen Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 615350 23768512 False 1 0;0;100 15.65 True ENSG00000173540 ENSG00000173540 HGNC:22932 HRAS gene HRAS Expert Review Red Cerebral malformation Neurology Schimmelpenning-Feuerstein-Mims syndrome, somatic mosaic, 163200;Hemimegalencephaly False 1 0;0;0 15.65 False ENSG00000174775 ENSG00000174775 HGNC:5173 KRAS gene KRAS Expert Review Red Cerebral malformation Neurology Schimmelpenning-Feuerstein-Mims syndrome, somatic mosaic, 163200;Hemimegalencephaly False 1 0;0;0 15.65 False ENSG00000133703 ENSG00000133703 HGNC:6407 MCF2 gene MCF2 Expert Review Red;Literature Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, biallelic mutations in females Perisylvian polymicrogyria;bilateral perisylvian polymicrogyria, MONDO:0020340 31846234 False 1 0;0;100 15.65 False ENSG00000101977 ENSG00000101977 HGNC:6940 MTOR gene MTOR Expert Review Red Cerebral malformation Neurology Segmental Overgrowth Syndrome;HME;Hemimegalencephaly False 1 0;0;0 15.65 False ENSG00000198793 ENSG00000198793 HGNC:3942 NODAL gene NODAL NHS GMS;Expert Review Red;Illumina TruGenome Clinical Sequencing Services Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 27363716 False 1 0;100;0 15.65 False ENSG00000156574 ENSG00000156574 HGNC:7865 NRAS gene NRAS Expert Review Red Cerebral malformation Neurology Schimmelpenning-Feuerstein-Mims syndrome, somatic mosaic, 163200;Hemimegalencephaly False 1 0;0;0 15.65 False ENSG00000213281 ENSG00000213281 HGNC:7989 PEX11A gene PEX11A Literature Cerebral malformation Neurology Unknown Zellweger syndrome;peroxisome proliferation;mild peroxisomal biogenesis defect 25177298;10716247;11839773;25608554 False 1 0;0;100 15.65 False ENSG00000166821 ENSG00000166821 HGNC:8852 PEX7 gene PEX7 Expert Review Red;NHS GMS;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Rhizomelic chondrodysplasia punctata type 1 (Peroxisomal disorders);Peroxisome biogenesis disorder 9B, 614879;Rhizomelic chondrodysplasia punctata, type 1, 215100 27604308 False 1 33;0;67 15.65 False ENSG00000112357 ENSG00000112357 HGNC:8860 POMK gene POMK Expert Review Red;Literature Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 12 615249 24925318 False 1 0;100;0 15.65 True ENSG00000185900 ENSG00000185900 HGNC:26267 SMAD2 gene SMAD2 NHS GMS;Expert Review Red;Radboud University Medical Center, Nijmegen Cerebral malformation Neurology Unknown Unknown (Roessler (2008) Am J Hum Genet 83,18) 18538293 False 1 0;0;100 15.65 False ENSG00000175387 ENSG00000175387 HGNC:6768 TBC1D7 gene TBC1D7 Expert Review Red Cerebral malformation Neurology BIALLELIC, autosomal or pseudoautosomal Macrocephaly/megalencephaly syndrome, autosomal recessive, OMIM:248000 False 1 100;0;0 15.65 False ENSG00000145979 ENSG00000145979 HGNC:21066 TSC2 gene TSC2 Expert Review Red;Literature Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Focal cortical dysplasia, type II, somatic 607341 28215400;19175396 False 1 0;0;0 15.65 False Other - please provide details in the comments ENSG00000103197 ENSG00000103197 HGNC:12363 ISCA-37430-Loss region Expert Review Green;ClinGen Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown microcephaly, dysgenesis of the corpus callosum, and cerebellar atrophy, as well as neurobehavioral disorders, including delayed development, mental retardation, and attention deficit-hyperactivity disorder. Patients with duplications of YWHAE tended to have macrosomia, facial dysmorphism, and mild developmental delay;growth restriction, craniofacial dysmorphisms, structural abnormalities of brain and cognitive impairment;Chromosome 17p13.3 duplication syndrome;prominent forehead, bitemporal hollowing, short nose with upturned nares, protuberant upper lip, thin vermilion border, and small jaw;Characteristic facies, pre- and post-natal growth retardation;247200;classic lissencephaly (pachygyria, incomplete or absent gyration of the cerebrum), microcephaly, wrinkled skin over the glabella and frontal suture, prominent occiput, narrow forehead, downward slanting palpebral fissures, small nose and chin, cardiac malformations, hypoplastic male extrenal genitalia, growth retardation, and mental deficiency with seizures and EEG abnormalities;Miller-Dieker lissencephaly syndrome False 3 0;0;0 15.65 False 17 1344539 2685615 3 60 cnv_loss 17p13.3 (Miller-Dieker syndrome) region (includes YWHAE and PAFAH1B1) Loss ISCA-46300-Loss region Expert Review Green;ClinGen Cerebral malformation Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Developmental delays/intellectual disability, brain anomalies, craniofacial abnormalities, hypermobile joints, digital findings, and other variable clinical features 27399968;22180641 False 3 100;0;0 15.65 False 15 75339446 75680568 3 60 cnv_loss 15q24 recurrent region (LCR C-LCR D) (includes SIN3A) Loss ISCA-46743-Loss region ClinGen;Expert Review Green Cerebral malformation Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) 30158690;33758131 False 3 100;0;0 15.65 False X 123900469 124102669 3 60 cnv_loss Xq25 region (includes STAG2) Loss