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 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Baraitser-Winter syndrome 1 (MIM#243310) 29671837;22366783 False 3 100;0;0 1.21 True ENSG00000075624 ENSG00000075624 HGNC:132 ACTG1 gene ACTG1 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Baraitser-Winter syndrome 2 (MIM#614583) 29671837;27240540;25052316 False 3 100;0;0 1.21 True ENSG00000184009 ENSG00000184009 HGNC:144 APC2 gene APC2 Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Cortical dysplasia, complex, with other brain malformations 10, MIM#618677 31585108 False 3 100;0;0 1.21 True ENSG00000115266 ENSG00000115266 HGNC:24036 ARX gene ARX Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders X-LINKED: hemizygous mutation in males, biallelic mutations in females Lissencephaly, X-linked 2, MIM# 300215 14722918 False 3 100;0;0 1.21 True ENSG00000004848 ENSG00000004848 HGNC:18060 ASPM gene ASPM Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Microcephaly 5, primary, autosomal recessive (MIM#608716)" 18452193;19332161;19770472;27250695 False 3 100;0;0 1.21 True ENSG00000066279 ENSG00000066279 HGNC:19048 B3GALNT2 gene B3GALNT2 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies, type A, 11, MIM# 615181 23453667 False 3 100;0;0 1.21 True ENSG00000162885 ENSG00000162885 HGNC:28596 B4GAT1 gene B4GAT1 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13 MIM# 615287 23359570;23877401;23359570;23217742 False 3 50;50;0 1.21 True ENSG00000174684 ENSG00000174684 HGNC:15685 CAMSAP1 gene CAMSAP1 Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Cortical dysplasia, complex, with other brain malformations 12, MIM# 620316 36283405 False 3 100;0;0 1.21 True ENSG00000130559 ENSG00000130559 HGNC:19946 CASP2 gene CASP2 Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Intellectual developmental disorder, autosomal recessive 80, with variant lissencephaly, MIM# 620653 PMID: 37880421 False 3 100;0;0 1.21 True ENSG00000106144 ENSG00000106144 HGNC:1503 CEP85L gene CEP85L Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Lissencephaly, posterior predominant 32097630 False 3 100;0;0 1.21 True ENSG00000111860 ENSG00000111860 HGNC:21638 CRADD gene CRADD Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 34, with variant lissencephaly, MIM# 614499 27773430 False 3 100;0;0 1.21 True ENSG00000169372 ENSG00000169372 HGNC:2340 CTNNA2 gene CTNNA2 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Cortical dysplasia, complex, with other brain malformations 9, MIM#618174 30013181 False 3 100;0;0 1.21 True ENSG00000066032 ENSG00000066032 HGNC:2510 DCHS1 gene DCHS1 Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Van Maldergem syndrome 1 (MIM#601390)" 27262615;22473091 False 3 100;0;0 1.21 True ENSG00000166341 ENSG00000166341 HGNC:13681 DCX gene DCX Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Lissencephaly, X-linked, MIM# 300067;Subcortical laminal heterotopia, X-linked 300067 10915612;9489699;12552055 False 3 100;0;0 1.21 True ENSG00000077279 ENSG00000077279 HGNC:2714 DYNC1H1 gene DYNC1H1 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Mental retardation, autosomal dominant 13, MIM# 614563 23603762;29671837;32570172;27331017 False 3 100;0;0 1.21 True ENSG00000197102 ENSG00000197102 HGNC:2961 EML1 gene EML1 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Band heterotopia (MIM# 600348) 31710781 False 3 100;0;0 1.21 True ENSG00000066629 ENSG00000066629 HGNC:3330 ISPD gene ISPD Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7, MIM# 614643 22522421;23217329 False 3 100;0;0 1.21 True ENSG00000214960 ENSG00000214960 HGNC:37276 KATNB1 gene KATNB1 Expert list;Expert Review Green Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal "Lissencephaly 6, with microcephaly, MIM# 616212" 25521378;25521379;26640080 False 3 100;0;0 1.21 True ENSG00000140854 ENSG00000140854 HGNC:6217 KIF2A gene KIF2A Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cortical dysplasia, complex, with other brain malformations 3, MIM# 615411 23603762;27896282;27747449;29077851;31919497 False 3 100;0;0 1.21 True ENSG00000068796 ENSG00000068796 HGNC:6318 KIF5C gene KIF5C Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cortical dysplasia, complex, with other brain malformations 2, MIM# 615282 23603762;23033978;32562872 False 3 100;0;0 1.21 True ENSG00000168280 ENSG00000168280 HGNC:6325 LAMA2 gene LAMA2 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal LAMA2-related muscular dystrophy;Muscular dystrophy, congenital, merosin deficient or partially deficient, MIM# 607855 20207543;18406646 False 3 100;0;0 1.21 True ENSG00000196569 ENSG00000196569 HGNC:6482 LAMB1 gene LAMB1 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Lissencephaly 5, MIM# 615191 23472759;25925986;29888467 False 3 100;0;0 1.21 True ENSG00000091136 ENSG00000091136 HGNC:6486 LARGE1 gene LARGE1 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 6, MIM# 613154;Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 6, MIM# 608840 False 3 100;0;0 1.21 True ENSG00000133424 ENSG00000133424 HGNC:6511 MACF1 gene MACF1 Expert list;Expert Review Green Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted "Lissencephaly 9 with complex brainstem malformation, MIM# 618325" 30471716 False 3 100;0;0 1.21 True 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 NDE1 gene NDE1 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Microhydranencephaly 605013;Lissencephaly 4 (with microcephaly) 614019 30637988 False 3 100;0;0 1.21 True ENSG00000072864 ENSG00000072864 HGNC:17619 OSGEP gene OSGEP Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Galloway-Mowat syndrome 3, MIM#617729 PMID: 30558655 False 3 100;0;0 1.21 True ENSG00000092094 ENSG00000092094 HGNC:18028 PAFAH1B1 gene PAFAH1B1 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Lissencephaly 1, MIM# 607432;Subcortical laminar heterotopia, MIM# 607432;MONDO:0011830 11754098;18285425 False 3 100;0;0 1.21 True ENSG00000007168 ENSG00000007168 HGNC:8574 PIDD1 gene PIDD1 Expert Review;Expert Review Green Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly, MIM# 619827 28397838;29302074;33414379;34163010 False 3 100;0;0 1.21 True ENSG00000177595 ENSG00000177595 HGNC:16491 RELN gene RELN Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Lissencephaly 2 (Norman-Roberts type), MIM# 257320 10973257;29671837;31805691;35769015 False 3 100;0;0 1.21 True ENSG00000189056 ENSG00000189056 HGNC:9957 SNAP29 gene SNAP29 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome (MIM#609528) 29051910;21073448;30793783 False 3 100;0;0 1.21 True ENSG00000099940 ENSG00000099940 HGNC:11133 TMEM5 gene TMEM5 Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 10, MIM# 615041 23217329;23519211 False 3 100;0;0 1.21 True ENSG00000118600 ENSG00000118600 HGNC:13530 TP73 gene TP73 Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Ciliary dyskinesia, primary, 47, and lissencephaly, MIM#619466;brain malformation;lissencephaly 34077761 False 3 100;0;0 1.21 True ENSG00000078900 ENSG00000078900 HGNC:12003 TUBA1A gene TUBA1A Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Lissencephaly 3, MIM#611603 30517687;20466733 False 3 100;0;0 1.21 True Other ENSG00000167552 ENSG00000167552 HGNC:20766 TUBGCP2 gene TUBGCP2 Expert Review Green;Literature Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Lissencephaly;pachygyria;subcortical band heterotopia;microcephaly;intellectual disability 31630790 False 3 100;0;0 1.21 True ENSG00000130640 ENSG00000130640 HGNC:18599 VLDLR gene VLDLR Australian Genomics Health Alliance Brain Malformations Flagship;Expert Review Green;Victorian Clinical Genetics Services Lissencephaly and Band Heterotopia Neurology and neurodevelopmental disorders BIALLELIC, autosomal or pseudoautosomal Cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1 (MIM#224050) 16080122;18364738;18326629;22700954;22973972 False 3 100;0;0 1.21 True ENSG00000147852 ENSG00000147852 HGNC:12698