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 ADD3 gene ADD3 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal "Cerebral palsy, spastic quadriplegic, 3 617008" Microcephaly;HP:0000252 PMID: 23836506;29768408 False 2 100;0;0 1.295 True ENSG00000148700 ENSG00000148700 HGNC:245 AKT3 gene AKT3 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Microcephaly Microcephaly;HP:0000252 32827175;31929334;30853971;30053339;25424989 False 2 0;100;0 1.295 True ENSG00000117020 ENSG00000117020 HGNC:393 BUB1 gene BUB1 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Primary microcephaly-30 (MCPH30), MIM#620183 Microcephaly;HP:0000252 35044816;19772675;19117986;23209306 False 2 0;100;0 1.295 True ENSG00000169679 ENSG00000169679 HGNC:1148 C7orf43 gene C7orf43 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal "Microcephaly 25, primary, autosomal recessive, MIM# 618351" Microcephaly;HP:0000252 30715179 False 2 0;100;0 1.295 True ENSG00000146826 ENSG00000146826 HGNC:25604 CCDC84 gene CCDC84 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Mosaic variegated aneuploidy syndrome 4 (MIM#620153) Microcephaly;HP:0000252 34009673 False 2 0;100;0 1.295 True ENSG00000186166 ENSG00000186166 HGNC:30460 CDK13 gene CDK13 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (MIM#617360) Microcephaly;HP:0000252 27479907;29021403;31238879 False 2 0;100;0 1.295 True ENSG00000065883 ENSG00000065883 HGNC:1733 CDK6 gene CDK6 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Microcephaly 12, primary, autosomal recessive, MIM#616080 Microcephaly;HP:0000252 23918663 False 2 0;100;0 1.295 True ENSG00000105810 ENSG00000105810 HGNC:1777 CDKL5 gene CDKL5 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Epileptic encephalopathy, early infantile, 2 (MIM#300672) Microcephaly;HP:0000252 15689447;19396824;22678952;31122804;30928302 False 2 0;100;0 1.295 True ENSG00000008086 ENSG00000008086 HGNC:11411 CEP63 gene CEP63 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Seckel syndrome 6, MIM#614728 Microcephaly;HP:0000252 21983783;26158450 False 2 0;100;0 1.295 True ENSG00000182923 ENSG00000182923 HGNC:25815 CHD4 gene CHD4 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Sifrim-Hitz-Weiss syndrome (MIM#617159) Microcephaly;HP:0000252 31388190 False 2 0;100;0 1.295 True ENSG00000111642 ENSG00000111642 HGNC:1919 CLTC gene CLTC Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Mental retardation, autosomal dominant 56 (MIM#617854) Microcephaly;HP:0000252 31776469 False 2 0;100;0 1.295 True ENSG00000141367 ENSG00000141367 HGNC:2092 COG3 gene COG3 Expert list;Expert Review Amber Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Congenital disorder of glycosylation, type IIbb, MIM# 620546 Microcephaly;HP:0000252 PMID: 37711075 False 2 0;100;0 1.295 True ENSG00000136152 ENSG00000136152 HGNC:18619 COPB2 gene COPB2 Expert list;Expert Review Amber Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal "Microcephaly 19, primary, autosomal recessive, MIM# 617800" Microcephaly;HP:0000252 37734708;29036432;34450031 False 2 0;100;0 1.295 True ENSG00000184432 ENSG00000184432 HGNC:2232 CYHR1 gene CYHR1 Expert Review Amber;Other Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder and microcephaly, MONDO:0700092, CYHR1-related Microcephaly;HP:0000252 False 2 0;100;0 1.295 True ENSG00000187954 ENSG00000187954 HGNC:17806 DCAF15 gene DCAF15 Expert Review Amber;Other Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Cornelia de Lange syndrome, MONDO:0016033, DCAF15-related Microcephaly;HP:0000252 False 2 0;100;0 1.295 True ENSG00000132017 ENSG00000132017 HGNC:25095 DNM1L gene DNM1L Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BOTH monoallelic and biallelic, autosomal or pseudoautosomal Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1, MIM#614388 Microcephaly;HP:0000252 17460227;26992161;30801875 False 2 0;100;0 1.295 True ENSG00000087470 ENSG00000087470 HGNC:2973 DROSHA gene DROSHA Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Neurodevelopmental disorder (MONDO#0700092), DROSHA-related Microcephaly;HP:0000252 35405010 False 2 0;100;0 1.295 True ENSG00000113360 ENSG00000113360 HGNC:17904 EHMT1 gene EHMT1 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Kleefstra syndrome 1 MIM#610253 Microcephaly;HP:0000252 PMID: 29228531;28361100;21910222;19264732 False 2 0;100;0 1.295 True ENSG00000181090 ENSG00000181090 HGNC:24650 ERCC5 gene ERCC5 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Cerebrooculofacioskeletal syndrome 3 MIM#616570 Microcephaly;HP:0000252 32052936;24700531 False 2 0;100;0 1.295 True ENSG00000134899 ENSG00000134899 HGNC:3437 FOXR1 gene FOXR1 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Postnatal microcephaly, progressive brain atrophy and global developmental delay Microcephaly;HP:0000252 34723967 False 2 0;100;0 1.295 True ENSG00000176302 ENSG00000176302 HGNC:29980 FRMD4A gene FRMD4A Expert Review;Expert Review Amber Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Intellectual disability;microcephaly;Corpus callosum, agenesis of, with facial anomalies and cerebellar ataxia, MIM# 616819 Microcephaly;HP:0000252 25388005;30214071 False 2 0;100;0 1.295 True ENSG00000151474 ENSG00000151474 HGNC:25491 KLHL7 gene KLHL7 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal PERCHING syndrome, MIM# 617055 Microcephaly;HP:0000252 27392078;29074562 False 2 0;100;0 1.295 True ENSG00000122550 ENSG00000122550 HGNC:15646 LINGO1 gene LINGO1 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 64, MIM# 618103 Microcephaly;HP:0000252 31668702 False 2 0;100;0 1.295 True ENSG00000169783 ENSG00000169783 HGNC:21205 MCM6 gene MCM6 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder, MONDO:0700092, MCM6-related Microcephaly;HP:0000252 PMID: 37198333 False 2 0;100;0 1.295 True ENSG00000076003 ENSG00000076003 HGNC:6949 MCM7 gene MCM7 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Meier-Gorlin syndrome;Microcephaly;Intellectual disability;Lipodystrophy;Adrenal insufficiency Microcephaly;HP:0000252 33654309;34059554 False 2 0;100;0 1.295 True ENSG00000166508 ENSG00000166508 HGNC:6950 MRE11 gene MRE11 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Nijmegen breakage syndrome-like severe microcephaly Microcephaly;HP:0000252 21227757 False 2 0;100;0 1.295 True ENSG00000020922 ENSG00000020922 HGNC:7230 NACC1 gene NACC1 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder with epilepsy, cataracts, feeding difficulties, and delayed brain myelination , MIM#617393 Microcephaly;HP:0000252 28132692 False 2 0;100;0 1.295 True ENSG00000160877 ENSG00000160877 HGNC:20967 NCAPD3 gene NCAPD3 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Microcephaly 22, primary, autosomal recessive, MIM# 617984 Microcephaly;HP:0000252 27737959 False 2 0;100;0 1.295 True ENSG00000151503 ENSG00000151503 HGNC:28952 NDUFA2 gene NDUFA2 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Mitochondrial complex I deficiency, nuclear type 13 - MIM#618235 Microcephaly;HP:0000252 28857146;32154054;18513682 False 2 0;100;0 1.295 True ENSG00000131495 ENSG00000131495 HGNC:7685 NSMCE2 gene NSMCE2 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal SECKEL SYNDROME 10 Microcephaly;HP:0000252 25105364 False 2 0;100;0 1.295 True ENSG00000156831 ENSG00000156831 HGNC:26513 NUP85 gene NUP85 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Primary microcephaly Microcephaly;HP:0000252 34170319 False 2 0;100;0 1.295 True ENSG00000125450 ENSG00000125450 HGNC:8734 PCGF2 gene PCGF2 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Turnpenny-Fry syndrome, MIM# 618371 Microcephaly;HP:0000252 30343942 False 2 0;100;0 1.295 True ENSG00000056661 ENSG00000277258 HGNC:12929 PDCD6IP gene PDCD6IP Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Microcephaly 29, primary, autosomal recessive, MIM# 620047 Microcephaly;HP:0000252 PMID: 32286682 False 2 0;50;50 1.295 True ENSG00000170248 ENSG00000170248 HGNC:8766 PHC1 gene PHC1 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Microcephaly 11, primary, autosomal recessive, MIM#615414 Microcephaly;HP:0000252 23418308 False 2 0;100;0 1.295 True ENSG00000111752 ENSG00000111752 HGNC:3182 PPP1R15B gene PPP1R15B Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Microcephaly, short stature, and impaired glucose metabolism 2, MIM# 616817 Microcephaly;HP:0000252 26159176;26307080;27640355 False 2 0;100;0 1.295 True ENSG00000158615 ENSG00000158615 HGNC:14951 PRIM1 gene PRIM1 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Primordial dwarfism-immunodeficiency-lipodystrophy syndrome, MIM# 620005 Microcephaly;HP:0000252 33060134 False 2 0;100;0 1.295 True ENSG00000198056 ENSG00000198056 HGNC:9369 RBL2 gene RBL2 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Severe motor and cognitive impairment;Intellectual disability;Brunet-Wagner neurodevelopmental syndrome MIM#619690 Microcephaly;HP:0000252 PMID: 33980986;32105419;9806916 False 2 0;100;0 1.295 True ENSG00000103479 ENSG00000103479 HGNC:9894 RRP7A gene RRP7A Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Microcephaly 28, primary, autosomal recessive MIM#619453 Microcephaly;HP:0000252 33199730 False 2 0;100;0 1.295 True ENSG00000189306 ENSG00000189306 HGNC:24286 RUSC2 gene RUSC2 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal "Mental retardation, autosomal recessive 61, MIM# 617773" Microcephaly;HP:0000252 27612186 False 2 0;100;0 1.295 True ENSG00000198853 ENSG00000198853 HGNC:23625 SEC31A gene SEC31A Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal "?Neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies, OMIM #618651" Microcephaly;HP:0000252 30464055 False 2 0;100;0 1.295 True ENSG00000138674 ENSG00000138674 HGNC:17052 SELENOI gene SELENOI Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal developmental delay;spasticity;periventricular white mater abnormalities;peripheral neuropathy;seizures;microcephaly;bifid uvula in some affected individuals Microcephaly;HP:0000252 28052917 False 2 0;100;0 1.295 True ENSG00000138018 ENSG00000138018 HGNC:29361 SLC25A19 gene SLC25A19 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Microcephaly, Amish type, MIM# 607196 Microcephaly;HP:0000252 12185364 False 2 0;100;0 1.295 True ENSG00000125454 ENSG00000125454 HGNC:14409 SOX5 gene SOX5 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Lamb-Shaffer syndrome, MIM#616803 Microcephaly;HP:0000252 PMID: 36861937 False 2 0;100;0 1.295 True ENSG00000134532 ENSG00000134532 HGNC:11201 STAG1 gene STAG1 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Mental retardation, autosomal dominant 47, MIM# 617635 Microcephaly;HP:0000252 28119487 False 2 0;100;0 1.295 True ENSG00000118007 ENSG00000118007 HGNC:11354 SV2A gene SV2A Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Developmental and epileptic encephalopathy 113, MIM# 620772 Microcephaly;HP:0000252 PMID: 37985816 False 2 0;100;0 1.295 True ENSG00000159164 ENSG00000159164 HGNC:20566 TRIT1 gene TRIT1 Expert Review Amber;Victorian Clinical Genetics Services Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Combined oxidative phosphorylation deficiency 35 MIM#617873 Microcephaly;HP:0000252 32088416;24901367;28185376;30977854 False 2 0;100;0 1.295 True ENSG00000043514 ENSG00000043514 HGNC:20286 VPS51 gene VPS51 Expert list;Expert Review Amber Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal "Pontocerebellar hypoplasia, type 13, MIM# 618606" Microcephaly;HP:0000252 30624672;31207318 False 2 0;100;0 1.295 True ENSG00000149823 ENSG00000149823 HGNC:1172 WNK3 gene WNK3 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes X-LINKED: hemizygous mutation in males, biallelic mutations in females Prieto syndrome, MIM# 309610 Microcephaly;HP:0000252 35678782 False 2 0;100;0 1.295 True ENSG00000196632 ENSG00000196632 HGNC:14543 ZNF668 gene ZNF668 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with poor growth, large ears, and dysmorphic facies, MIM# 620194 Microcephaly;HP:0000252 34313816;26633546 False 2 0;100;0 1.295 True ENSG00000167394 ENSG00000167394 HGNC:25821 ZNRF3 gene ZNRF3 Expert Review Amber;Literature Microcephaly Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted complex neurodevelopmental disorder MONDO:0100038 Microcephaly;HP:0000252 39168120 False 2 0;100;0 1.295 True ENSG00000183579 ENSG00000183579 HGNC:18126