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 ANKH gene ANKH Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Craniometaphyseal dysplasia, OMIM:123000;craniosynostosis, MONDO:0015469 36118902;36980886 False 2 0;100;0 6.4 False ENSG00000154122 ENSG00000154122 HGNC:15492 ASXL3 gene ASXL3 Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Bainbridge-Ropers syndrome, OMIM:615485;craniosynostosis, MONDO:0015469 24044690;33288889 False 2 0;100;0 6.4 False ENSG00000141431 ENSG00000141431 HGNC:29357 AXIN2 gene AXIN2 Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Oligodontia-colorectal cancer syndrome, OMIM:608615;craniosynostosis, MONDO:0015469 15790973;30088857;30976280;34134783 False 2 0;67;33 6.4 False ENSG00000168646 ENSG00000168646 HGNC:904 CHD5 gene CHD5 Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Parenti-Mignot neurodevelopmental syndrome, OMIM:610771;Intellectual disability, MONDO:0001071;Epilepsy, MONDO:0005027 33944996 False 2 100;0;0 6.4 False ENSG00000116254 ENSG00000116254 HGNC:16816 DDX3X gene DDX3X Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Intellectual developmental disorder, X-linked syndromic, Snijders Blok type, OMIM:300958;craniosynostosis, MONDO:0015469 30936465;32530565;33789733;36980886 False 2 0;100;0 6.4 False ENSG00000215301 ENSG00000215301 HGNC:2745 DPF2 gene DPF2 Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 29429572 False 2 0;100;0 6.4 False ENSG00000133884 ENSG00000133884 HGNC:9964 DPH1 gene DPH1 Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Developmental delay with short stature, dysmorphic facial features, and sparse hair, OMIM:616901 26220823;30877278 False 2 0;100;0 6.4 False ENSG00000108963 ENSG00000108963 HGNC:3003 ESCO2 gene ESCO2 Expert list;Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal Roberts syndrome;SC phocomelia syndrome 31192177 False 2 0;67;33 6.4 True ENSG00000171320 ENSG00000171320 HGNC:27230 FGF10 gene FGF10 Expert list;Expert Review Amber Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted craniosynostosis, MONDO:0015469 29215649 False 2 0;100;0 6.4 False ENSG00000070193 ENSG00000070193 HGNC:3666 FREM1 gene FREM1 Expert list;Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Trigonocephaly 2, OMIM:614485 21931569;33038106;33288889;33937142 False 2 0;50;50 6.4 True ENSG00000164946 ENSG00000164946 HGNC:23399 GPC3 gene GPC3 Expert list;Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females Simpson-Golabi-Behmel syndrome, type 1, OMIM:312870 19372699;24115482;25804025;34429528 False 2 0;80;20 6.4 True ENSG00000147257 ENSG00000147257 HGNC:4451 IRX5 gene IRX5 Expert Review;Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Hamamy syndrome, OMIM:611174 22581230;29168297 False 2 0;80;20 6.4 True ENSG00000176842 ENSG00000176842 HGNC:14361 KPTN gene KPTN Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Intellectual developmental disorder, autosomal recessive 41, OMIM:615637;craniosynostosis, MONDO:0015469 24239382;36980886 False 2 0;100;0 6.4 False ENSG00000118162 ENSG00000118162 HGNC:6404 MASP1 gene MASP1 Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 3MC syndrome 1, OMIM:257920;3MC syndrome 1, MONDO:0009770 30601195;29407414;26419238;21035106;21258343;26789649 False 2 20;80;0 6.4 False ENSG00000127241 ENSG00000127241 HGNC:6901 OGT gene OGT Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females Intellectual developmental disorder, X-linked 106, OMIM:300997 32530565;34429528 False 2 0;100;0 6.4 False ENSG00000147162 ENSG00000147162 HGNC:8127 PJA1 gene PJA1 Expert list;Expert Review Amber Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Trigonocephaly;Intellectual disability;Neurodevelopmental disorders 32530565 False 2 0;100;0 6.4 False ENSG00000181191 ENSG00000181191 HGNC:16648 PPP1CB gene PPP1CB Expert list;Expert Review Amber Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Noonan syndrome-like disorder with loose anagen hair 2 617506 False 2 0;100;0 6.4 False ENSG00000213639 ENSG00000213639 HGNC:9282 SEC24D gene SEC24D Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Cole-Carpenter syndrome 2 616294 25683121;30462379;27942778 False 2 0;100;0 6.4 False ENSG00000150961 ENSG00000150961 HGNC:10706 SHOC2 gene SHOC2 Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal Noonan-like syndrome with loose anagen hair 607721 25123707 False 2 0;100;0 6.4 False ENSG00000108061 ENSG00000108061 HGNC:15454 SMAD3 gene SMAD3 Expert list;Expert Review Amber Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Loeys-Dietz syndrome 3, OMIM:613795 20301312;29392890;31569402;32935439;36980886 False 2 33;67;0 6.4 False ENSG00000166949 ENSG00000166949 HGNC:6769 SPRY1 gene SPRY1 Expert Review Amber;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal craniosynostosis, MONDO:0015469 36543535 False 2 0;100;0 6.4 False ENSG00000164056 ENSG00000164056 HGNC:11269 ISCA-37420-Loss region Expert Review Amber;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Koolen-De Vries syndrome, OMIM:610443;Developmental delay/intellectual disability, hypotonia, distinctive facial features, congenital malformations, and behavioural feature 26424144;21094706;19447831 False 2 0;100;0 6.4 False 17 45627800 46087514 3 60 cnv_loss 17q21.3 recurrent region (includes KANSL1) Loss