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 ATP11A gene ATP11A Expert Review Red;Literature Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder 34403372 False 1 0;100;0 8.43 False ENSG00000068650 ENSG00000068650 HGNC:13552 ATRIP gene ATRIP Expert list;Expert Review Red;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephalic primordial dwarfism;Severe microcephaly (-10 SD), micrognathia, dental crowding, small earlobes, delayed bone age, and symmetric dwarfism 23144622 False 1 0;100;0 8.43 False ENSG00000164053 ENSG00000164053 HGNC:33499 CDC6 gene CDC6 Expert list;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Meier-Gorlin syndrome 5, OMIM:613805;Microcephalic primordial dwarfism 21358632;22333897 False 1 0;50;50 8.43 False ENSG00000094804 ENSG00000094804 HGNC:1744 CDK6 gene CDK6 Literature;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Autosomal recessive primary microcephaly (MCPH) ;?Microcephaly 12, primary, autosomal recessive, 616080 25951892; 25548773; 23918663 False 1 0;100;0 8.43 False ENSG00000105810 ENSG00000105810 HGNC:1777 CENPE gene CENPE Expert list;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal ?Microcephaly 13, primary, autosomal recessive, OMIM:616051;Microcephalic primordial dwarfism False 1 0;100;0 8.43 False ENSG00000138778 ENSG00000138778 HGNC:1856 CEP63 gene CEP63 Expert list;Expert Review Red;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal MCPH;primary microcephaly;?Seckel syndrome 6, OMIM:614728;Microcephaly 21983783;26158450 False 1 33;67;0 8.43 False ENSG00000182923 ENSG00000182923 HGNC:25815 COPB2 gene COPB2 Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly, HP:0000252 29036432 False 1 0;0;100 8.43 False ENSG00000184432 ENSG00000184432 HGNC:2232 DPP6 gene DPP6 Expert list;Expert Review Red;NHS GMS Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Intellectual developmental disorder, autosomal dominant 33, OMIM:616311 21943606;23832105;29651237 False 1 0;100;0 8.43 False ENSG00000130226 ENSG00000130226 HGNC:3010 EOMES gene EOMES Literature;NHS GMS Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal microcephaly syndrome 17353897 False 1 0;50;50 8.43 False ENSG00000163508 ENSG00000163508 HGNC:3372 FANCM gene FANCM Expert Review Red;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Fanconi anemia 16116422 Meetei et al., 2005 paper that originally classified FANCM as a Fanconi anemia gene; 19423727 Singh et al., 2009 reclassified the Meetei et al, patients as having FANCA; 25078778 Lim et al., 2014 did NOT find evidence to support FANCM as a gene associated with Fanconi anemia. False 1 0;100;0 8.43 False ENSG00000187790 ENSG00000187790 HGNC:23168 GINS2 gene GINS2 Expert Review Red;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Meier-Gorlin syndrome like;Meier-Gorlin syndrome, MONDO:0016817 34353863 False 1 0;100;0 8.43 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000131153 ENSG00000131153 HGNC:24575 HIKESHI gene HIKESHI Expert list;Expert Review Red Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Leukodystrophy, hypomyelinating, 13, OMIM:616881 26545878;28000699 False 1 100;0;0 8.43 False ENSG00000149196 ENSG00000149196 HGNC:26938 NCAPH gene NCAPH Expert Review Red;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly 23, primary, autosomal recessive, 617985 27737959 False 1 0;0;0 8.43 False ENSG00000121152 ENSG00000121152 HGNC:1112 NIN gene NIN Expert Review Red;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal ?Seckel syndrome 7, 614851; SCKL7 22933543 False 1 0;100;0 8.43 False ENSG00000100503 ENSG00000100503 HGNC:14906 NSMCE2 gene NSMCE2 NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Seckel syndrome 10, 617253; SCKL10 25105364 False 1 0;100;0 8.43 False ENSG00000156831 ENSG00000156831 HGNC:26513 NUF2 gene NUF2 Expert Review Red;Literature Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted microcephaly;short stature;bilateral vocal cord paralysis;micrognathia;atrial septal defect 33721060 False 1 0;0;100 8.43 False ENSG00000143228 ENSG00000143228 HGNC:14621 PCLO gene PCLO Expert list;NHS GMS Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Pontocerebellar hypoplasia, type 3, 608027 12771259;25832664 False 1 0;0;100 8.43 False ENSG00000186472 ENSG00000186472 HGNC:13406 PHC1 gene PHC1 Expert list;Literature;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Autosomal recessive primary microcephaly (MCPH) ;?Microcephaly 11, primary, autosomal recessive, 615414;MCPH; primary microcephaly 25951892; 25548773 False 1 0;100;0 8.43 False ENSG00000111752 ENSG00000111752 HGNC:3182 PLAA gene PLAA Expert Review Red;NHS GMS;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies, 617527 28007986;28413018 False 1 0;100;0 8.43 False ENSG00000137055 ENSG00000137055 HGNC:9043 PPP1R35 gene PPP1R35 Expert Review Red;Other Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Primary microcephaly False 1 0;0;0 8.43 False ENSG00000160813 ENSG00000160813 HGNC:28320 RING1 gene RING1 Literature Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown microcephaly;intellectual disability 29386386 False 1 0;0;100 8.43 False ENSG00000204227 ENSG00000204227 HGNC:10018 RUSC2 gene RUSC2 Expert list;Expert Review Red Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 61, MIM# 617773 27612186 False 1 0;50;50 8.43 False ENSG00000198853 ENSG00000198853 HGNC:23625 SMO gene SMO Expert list;Expert Review Red Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly HP:0000252;postaxial polydactyly MONDO:0020927;congenital heart disease MONDO:0005453;Hirschsprung disease MONDO:0018309 32413283 False 1 100;0;0 8.43 False ENSG00000128602 ENSG00000128602 HGNC:11119 TCF4 gene TCF4 Expert list;Expert Review Red Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Pitt-Hopkins syndrome, OMIM:610954 18728071;21671391;29318938 False 1 50;50;0 8.43 False ENSG00000196628 ENSG00000196628 HGNC:11634 TPR gene TPR Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Microcephaly, MONDO:0001149 34494102 False 1 0;0;100 8.43 False ENSG00000047410 ENSG00000047410 HGNC:12017 TPRKB gene TPRKB Expert list;Expert Review Red Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Galloway-Mowat syndrome 5, OMIM:617731 28805828 False 1 50;0;50 8.43 False ENSG00000144034 ENSG00000144034 HGNC:24259 TRMT1 gene TRMT1 Literature;NHS GMS Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal Non syndromal congenital microcephaly 30289604 False 1 0;50;50 8.43 False ENSG00000104907 ENSG00000104907 HGNC:25980 TUBGCP3 gene TUBGCP3 Expert list;NHS GMS Severe microcephaly Neurology MCPH; primary microcephaly False 1 0;100;0 8.43 False ENSG00000126216 ENSG00000126216 HGNC:18598 WDFY3 gene WDFY3 Expert Review Red;NHS GMS;Other Severe microcephaly Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ?Microcephaly 18, primary, autosomal dominant, 617520 27008544 False 1 0;100;0 8.43 False ENSG00000163625 ENSG00000163625 HGNC:20751 ZNHIT3 gene ZNHIT3 Expert list;NHS GMS Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal PEHO syndrome, 260565;microcephaly 28335020 False 1 0;0;100 8.43 False ENSG00000108278 ENSG00000273611 HGNC:12309 ZPR1 gene ZPR1 Expert Review Red;Literature Severe microcephaly Neurology BIALLELIC, autosomal or pseudoautosomal ?Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies, OMIM:619321 29851065 False 1 0;0;100 8.43 False ENSG00000109917 ENSG00000109917 HGNC:13051