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 list;Expert Review Green Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Baraitser-Winter syndrome 1, OMIM:243310;Baraitser-Winter syndrome 1, MONDO:0009470 22366783;23649928;23756437 False 3 100;0;0 6.4 False ENSG00000075624 ENSG00000075624 HGNC:132 ACTG1 gene ACTG1 Expert Review Green;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Baraitser-Winter syndrome 2, OMIM:614583 22366783;25052316;27240540 False 3 100;0;0 6.4 False ENSG00000184009 ENSG00000184009 HGNC:144 ADAMTSL4 gene ADAMTSL4 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Ectopia lentis 225200/225100;craniosynostosis with ectopia lentis, MONDO:0011347 10215540;20702823;22871183;28642162;35378950 False 3 60;20;20 6.4 True ENSG00000143382 ENSG00000143382 HGNC:19706 AHDC1 gene AHDC1 Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Xia-Gibbs syndrome, OMIM:615829 27884935;30152016;30858058 False 3 75;25;0 6.4 False ENSG00000126705 ENSG00000126705 HGNC:25230 ALPL gene ALPL Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Hypophosphatasia, adult, OMIM:146300;Hypophosphatasia, childhood, OMIM:241510;Hypophosphatasia, infantile, OMIM:241500 19232125;18769927 False 3 67;33;0 6.4 False ENSG00000162551 ENSG00000162551 HGNC:438 ALX4 gene ALX4 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Parietal foramina;Parietal foramina 2, (AD), 609597;Frontonasal dysplasia 2, (AR), 613451 22829454;29681084;29215649 False 3 50;25;25 6.4 True ENSG00000052850 ENSG00000052850 HGNC:450 ARID1B gene ARID1B Expert Review Green;Literature;NHS GMS;Research Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Coffin-Siris syndrome 1, OMIM:135900 27474218;32530565;34429528;36118902;36980886 False 3 100;0;0 6.4 False ENSG00000049618 ENSG00000049618 HGNC:18040 ARSB gene ARSB Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Mucopolysaccharidosis VI (MPS6) 253200 30083803 False 3 50;50;0 6.4 False ENSG00000113273 ENSG00000113273 HGNC:714 ASXL1 gene ASXL1 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Bohring-Opitz syndrome, OMIM:605039;Bohring-Opitz syndrome, MONDO:0011510 21706002 False 3 67;33;0 6.4 True ENSG00000171456 ENSG00000171456 HGNC:18318 B3GAT3 gene B3GAT3 Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Craniosynostosis and bone fragility;Multiple joint dislocations, short stature, craniofacial dysmorphism, with or without congenital heart defects OMIM:245600;Larsen-like syndrome, B3GAT3 type MONDO:0009511 28771243;31438591;31196143 False 3 75;25;0 6.4 False ENSG00000149541 ENSG00000149541 HGNC:923 BCL11B gene BCL11B Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Intellectual developmental disorder with dysmorphic facies, speech delay, and T-cell abnormalities, OMIM:618092;Craniosynostosis, MONDO:0015469 31067316;34900871;36275064;36470856;36512050;36980886 False 3 100;0;0 6.4 False ENSG00000127152 ENSG00000127152 HGNC:13222 BRAF gene BRAF Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted cardiofaciocutaneous syndrome type 115150;Noonan syndrome type 7 613706 28650561 False 3 50;50;0 6.4 False ENSG00000157764 ENSG00000157764 HGNC:1097 CDC45 gene CDC45 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Coronal synostosis;Meier-Gorlin syndrome 7, 617063 25985138 False 3 67;33;0 6.4 True ENSG00000093009 ENSG00000093009 HGNC:1739 CDK13 gene CDK13 Expert Review Green;Literature;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder, OMIM:617360;craniosynostosis, MONDO:0015469 28807008;33288889;34429528 False 3 100;0;0 6.4 False ENSG00000065883 ENSG00000065883 HGNC:1733 CHD7 gene CHD7 Expert Review;Expert Review Green Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted CHARGE syndrome, OMIM:214800;CHARGE syndrome, MONDO:0008965 33844462;30498854;33288889;24975120;22363697 False 3 50;50;0 6.4 False ENSG00000171316 ENSG00000171316 HGNC:20626 COLEC11 gene COLEC11 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 265050;3MC syndrome 2 265050 21258343 False 3 67;33;0 6.4 True ENSG00000118004 ENSG00000118004 HGNC:17213 CTSK gene CTSK Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Pycnodysostosis 265800;265800 21968522;23175007 False 3 67;33;0 6.4 True ENSG00000143387 ENSG00000143387 HGNC:2536 CYP26B1 gene CYP26B1 Expert list;Expert Review Green;NHS GMS;Radboud University Medical Center, Nijmegen Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Craniosynostosis with radiohumeral fusions and other skeletal and craniofacial anomalies, 614416 22019272;27410456 False 3 33;33;33 6.4 True ENSG00000003137 ENSG00000003137 HGNC:20581 EFNB1 gene EFNB1 Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS 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) Craniofrontonasal dysplasia, OMIM:304110 15166289;23335590;15124102 False 3 67;33;0 6.4 True Other - please provide details in the comments ENSG00000090776 ENSG00000090776 HGNC:3226 ERF gene ERF Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Craniosynostosis 4, 600775;Craniosynostosis 4 26097063;23354439 False 3 67;33;0 6.4 True ENSG00000105722 ENSG00000105722 HGNC:3444 FAM20C gene FAM20C Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Raine syndrome 259775 19250384 False 3 33;33;33 6.4 True ENSG00000177706 ENSG00000177706 HGNC:22140 FBN1 gene FBN1 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Marfan syndrome, OMIM:154700;Marfan lipodystrophy syndrome, OMIM:616914;craniosynostosis, MONDO:0015469 16596670;24039054;27884935;29168297;31754721 False 3 60;20;20 6.4 True ENSG00000166147 ENSG00000166147 HGNC:3603 FBXO11 gene FBXO11 Expert Review Green;Literature;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities, OMIM:618089 30057029;34429528 False 3 100;0;0 6.4 False ENSG00000138081 ENSG00000138081 HGNC:13590 FGF9 gene FGF9 Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Multiple synostoses syndrome 3, OMIM:612961 12140681;19589401;28730625 False 3 75;0;25 6.4 False ENSG00000102678 ENSG00000102678 HGNC:3687 FGFR1 gene FGFR1 Eligibility statement prior genetic testing;Expert list;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Craniosynostosis 7874169;15625620 False 3 67;33;0 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000077782 ENSG00000077782 HGNC:3688 FGFR2 gene FGFR2 Eligibility statement prior genetic testing;Expert list;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;NHS GMS;Radboud University Medical Center, Nijmegen Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Crouzon syndrome, 123500; Jackson-Weiss syndrome, 123150; Beare-Stevenson cutis gyrata syndrome, 123790; Pfeiffer syndrome, 101600; Apert syndrome, 101200; Saethre-Chotzen; Craniosynostosis, nonspecific syndrome, 101400; Gastric cance;Craniosynostosis 7719344;7987400;7719345;8696350;22387015 False 3 67;33;0 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000066468 ENSG00000066468 HGNC:3689 FGFR3 gene FGFR3 Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Muenke syndrome;Crouzon syndrome with acanthosis nigricans 9042914;7493034 False 3 67;33;0 6.4 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000068078 ENSG00000068078 HGNC:3690 FLNA gene FLNA Expert list;Expert Review Green;NHS GMS 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) Frontometaphyseal dysplasia 1, OMIM:305620;Melnick-Needles syndrome, OMIM:309350;Otopalatodigital syndrome, type I, OMIM:311300;Otopalatodigital syndrome, type II, OMIM:304120 25873011 False 3 67;33;0 6.4 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000196924 ENSG00000196924 HGNC:3754 GLI3 gene GLI3 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Greig cephalopolysyndactyly syndrome, OMIM:175700 21326280;20583172 False 3 67;33;0 6.4 False ENSG00000106571 ENSG00000106571 HGNC:4319 GNAS gene GNAS Expert Review;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, maternally imprinted (paternal allele expressed) 103580;pseudohypoparathyroidism type 1a 103580;pseudohypoparathyroidism type 1a 19530187;26340332;26267576 False 3 50;25;25 6.4 True ENSG00000087460 ENSG00000087460 HGNC:4392 GNPTAB gene GNPTAB Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 252500;Mucolipidosis II alpha/beta(I cell disease) 252500 24891900 False 3 67;33;0 6.4 True ENSG00000111670 ENSG00000111670 HGNC:29670 HNRNPK gene HNRNPK Expert list;Expert Review Green Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Au-Kline syndrome, OMIM:616580 26173930;26954065;28771707;29904177;24501764;25348648;28374925;32588992 False 3 100;0;0 6.4 False ENSG00000165119 ENSG00000165119 HGNC:5044 HUWE1 gene HUWE1 Expert list;Expert Review Green;NHS GMS 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) X-linked intellectual disability with CSS 25985138;25590979;29180823 False 3 67;33;0 6.4 True ENSG00000086758 ENSG00000086758 HGNC:30892 IDS gene IDS Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females Mucopolysaccharidosis II (MPS2, Hunter syndrome) 309900;309900 15314824 False 3 67;33;0 6.4 True ENSG00000010404 ENSG00000010404 HGNC:5389 IDUA gene IDUA Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 607016;Mucopolysaccharidosis Ih/s (Hurler syndrome) 607014;607014 23917744 False 3 67;33;0 6.4 True ENSG00000127415 ENSG00000127415 HGNC:5391 IFT122 gene IFT122 Expert Review;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Cranioectodermal dysplasia type 1 OMIM:218330;cranioectodermal dysplasia 1 MONDO:0021093 20493458;24689072;26792575;29037998;23826986;33717254 False 3 33;33;33 6.4 True ENSG00000163913 ENSG00000163913 HGNC:13556 IFT140 gene IFT140 Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Short-rib thoracic dysplasia 9 with or without polydactyly, OMIM:266920 22503633;27874174;28288023;32007091 False 3 50;50;0 6.4 False ENSG00000187535 ENSG00000187535 HGNC:29077 IHH gene IHH Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Syndactyly, type 1, with or without craniosynostosis, OMIM:185900;Chr2q35dup syndrome 25692887;21167467 False 3 67;33;0 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000163501 ENSG00000163501 HGNC:5956 IL11RA gene IL11RA Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Craniosynostosis and dental anomalies, 614188;Craniosynostosis And Dental Anomalies 21741611;24002815;24498618 False 3 67;33;0 6.4 True ENSG00000137070 ENSG00000137070 HGNC:5967 IL6ST gene IL6ST Expert Review Green;Literature;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Hyper-IgE recurrent infection syndrome 4B, autosomal recessive, OMIM:618523 28747427;32566365 False 3 100;0;0 6.4 False ENSG00000134352 ENSG00000134352 HGNC:6021 JAG1 gene JAG1 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Alagille syndrome 1, OMIM:118450 23337010;12244552;29530693 False 3 33;33;33 6.4 True ENSG00000101384 ENSG00000101384 HGNC:6188 KAT6A gene KAT6A Expert Review;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Mental retardation (with Craniosynostosis), 616268 25728775;25728777 False 3 67;33;0 6.4 True ENSG00000083168 ENSG00000083168 HGNC:13013 KAT6B gene KAT6B Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted KAT6B-related disorders;Genitopatellar syndrome, OMIM:606170 28696035;33288889 False 3 75;25;0 6.4 False ENSG00000156650 ENSG00000156650 HGNC:17582 KMT2D gene KMT2D Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Kabuki syndrome 1, OMIM:147920 20672944;21280141 False 3 67;33;0 6.4 False ENSG00000167548 ENSG00000167548 HGNC:7133 KRAS gene KRAS Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted cardiofaciocutaneous syndrome type 2 615278;Noonan syndrome type 3 609942;615278;609942 19396835;22488932 False 3 67;33;0 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000133703 ENSG00000133703 HGNC:6407 LTBP1 gene LTBP1 Expert Review Green;Literature Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Cutis laxa, autosomal recessive, type IIE, OMIM:619451;craniosynostosis, MONDO:0015469 33991472 False 3 100;0;0 6.4 False ENSG00000049323 ENSG00000049323 HGNC:6714 MAN2B1 gene MAN2B1 Expert Review Green;Literature;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Mannosidosis, alpha-, types I and II, OMIM:248500 33288889;34429528;35242565 False 3 100;0;0 6.4 False ENSG00000104774 ENSG00000104774 HGNC:6826 MEGF8 gene MEGF8 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 614976;Carpenter 2 614976 23063620 False 3 67;33;0 6.4 True ENSG00000105429 ENSG00000105429 HGNC:3233 MSX2 gene MSX2 Expert list;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;NHS GMS;Radboud University Medical Center, Nijmegen Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Craniosynostosis, type 2, 604757;Parietal foramina 1, 168500;Parietal foramina with cleidocranial dysplasia, 168550;Craniosynostosis;MSX2-related craniosynostosis 8106171;23949913;23918290 False 3 67;33;0 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000120149 ENSG00000120149 HGNC:7392 NFIA gene NFIA Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Metopic synostosis, hydrocephalus, thin corpus callosum, mild developmental delay, autism, macrocephaly 35080095;31754721;33288889 False 3 50;50;0 6.4 False ENSG00000162599 ENSG00000162599 HGNC:7784 NFIX gene NFIX Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Malan syndrome, OMIM:614753;Marshall-Smith syndrome, OMIM:602535;craniosynostosis, MONDO:0015469 33288889;35997807 False 3 75;25;0 6.4 False ENSG00000008441 ENSG00000008441 HGNC:7788 P4HB gene P4HB Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cole-Carpenter syndrome 1 112240 25683117;29384951 False 3 50;50;0 6.4 False ENSG00000185624 ENSG00000185624 HGNC:8548 PHEX gene PHEX Expert Review;Expert Review Green;NHS GMS 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) X-linked hypophosphataemic rickets 17551721;19242361 False 3 67;33;0 6.4 True ENSG00000102174 ENSG00000102174 HGNC:8918 POR gene POR Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 201750;Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis 201750 14758361 False 3 67;33;0 6.4 True ENSG00000127948 ENSG00000127948 HGNC:9208 PRRX1 gene PRRX1 Expert Review;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Agnathia-otocephaly complex, OMIM:202650;craniosynostosis, MONDO:0015469;craniosynostosis, various combinations of sutures 36980886;37154149 False 3 60;20;20 6.4 False ENSG00000116132 ENSG00000116132 HGNC:9142 PTCH1 gene PTCH1 Expert Review;Expert Review Green Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted metopic craniosynostosis 31578813 False 3 50;50;0 6.4 False ENSG00000185920 ENSG00000185920 HGNC:9585 PTPN11 gene PTPN11 Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Noonan syndrome type 1 163950;leopard syndrome 151100 28650561 False 3 50;50;0 6.4 False ENSG00000179295 ENSG00000179295 HGNC:9644 RAB23 gene RAB23 Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Carpenter syndrome 201000;201000 17503333 False 3 67;33;0 6.4 True ENSG00000112210 ENSG00000112210 HGNC:14263 RECQL4 gene RECQL4 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 218600;Baller-Gerold syndrome 218600 24635570 False 3 67;33;0 6.4 True ENSG00000160957 ENSG00000160957 HGNC:9949 RNU12 gene RNU12 Expert Review Green;Literature;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal CDAGS syndrome, OMIM:603116;craniosynostosis-anal anomalies-porokeratosis syndrome, MONDO:001128 34085356 False 3 100;0;0 6.4 False ENSG00000270022 ENSG00000276027 HGNC:19380 RSPRY1 gene RSPRY1 Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Spondyloepimetaphyseal dysplasia, Faden-Alkuraya type, OMIM:616723 26365341;30063090 False 3 50;50;0 6.4 False ENSG00000159579 ENSG00000159579 HGNC:29420 RUNX2 gene RUNX2 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Craniosynostosis;156510 20683987;23307468;23348268 False 3 50;25;25 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000124813 ENSG00000124813 HGNC:10472 SIX1 gene SIX1 Expert Review;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted sagittal synostosis, multi-suture synostosis 33436522 False 3 33;67;0 6.4 False ENSG00000126778 ENSG00000126778 HGNC:10887 SKI gene SKI Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Shprintzen-Goldberg syndrome 182212;182212 23023332;23103230;24736733 False 3 67;33;0 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000157933 ENSG00000157933 HGNC:10896 SLC25A24 gene SLC25A24 Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Fontaine progeroid syndrome, OMIM;612289;Fontaine progeroid syndrome, MONDO:0012853 29903433;29100093;29100094 False 3 50;50;0 6.4 False ENSG00000085491 ENSG00000085491 HGNC:20662 SMAD6 gene SMAD6 Expert Review Green;Literature;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted metopic synostosis;sagittal synostosis;{Craniosynostosis 7, susceptibility to} 617439 27606499;23438589;28808027;28659821 False 3 67;33;0 6.4 False ENSG00000137834 ENSG00000137834 HGNC:6772 SMO gene SMO Expert Review Green;Literature;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Curry-Jones syndrome, somatic mosaic, 601707 27236920 False 3 67;33;0 6.4 False Other - please provide details in the comments ENSG00000128602 ENSG00000128602 HGNC:11119 SOX6 gene SOX6 Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Tolchin-Le Caignec syndrome, OMIM:618971;craniosynostosis 16258006;32442410;36118902;36980886 False 3 60;20;20 6.4 False ENSG00000110693 ENSG00000110693 HGNC:16421 SPECC1L gene SPECC1L Expert Review;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Opitz GBBB syndrome, type II 145410 25412741;26111080 False 3 33;33;33 6.4 True ENSG00000100014 ENSG00000100014 HGNC:29022 STAT3 gene STAT3 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Hyper IgE recurrent infection syndrome 147060;147060 20159255 False 3 67;33;0 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000168610 ENSG00000168610 HGNC:11364 TCF12 gene TCF12 Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Craniosynostosis 3, 615314;Craniosynostosis 3 23354436;25271085;24736737 False 3 67;33;0 6.4 True ENSG00000140262 ENSG00000140262 HGNC:11623 TFAP2B gene TFAP2B Expert Review;Expert Review Green Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Char syndrome 169100 31405973;31292255 False 3 0;0;0 6.4 False ENSG00000008196 ENSG00000008196 HGNC:11743 TGFBR1 gene TGFBR1 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Loeys-Dietz syndrome 1 609192;609192 15731757 False 3 67;33;0 6.4 True Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000106799 ENSG00000106799 HGNC:11772 TGFBR2 gene TGFBR2 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 610168;Loeys-Dietz syndrome 2 610168 15731757 False 3 67;33;0 6.4 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000163513 ENSG00000163513 HGNC:11773 TLK2 gene TLK2 Expert Review Green;Literature;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Mental retardation, autosomal dominant 57, OMIM:618050;Mental retardation, autosomal dominant 57, MONDO:0054837 27479843;29861108 False 3 50;50;0 6.4 False ENSG00000146872 ENSG00000146872 HGNC:11842 TMCO1 gene TMCO1 Expert Review;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MR syndrome;Cerebrofaciothoracic dysplasia/ craniofacial dysmorphism;skeletal anomalies;Craniofacial dysmorphism, skeletal anomalies, and mental retardation syndrome, 213980 20018682;24424126;24194475 False 3 33;33;33 6.4 True ENSG00000143183 ENSG00000143183 HGNC:18188 TRAF7 gene TRAF7 Expert Review;Expert Review Green Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted craniosynostosis 32376980 False 3 100;0;0 6.4 False ENSG00000131653 ENSG00000131653 HGNC:20456 TWIST1 gene TWIST1 Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS;Radboud University Medical Center, Nijmegen Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Saethre-Chotzen syndrome, 101400; Saethre-Chotzen syndrome with eyelid anomalies, 101400; Craniosynostosis, type 1, 123100; Robinow-Sorauf syndrome, 180750 8988166;8988167 False 3 67;33;0 6.4 True ENSG00000122691 ENSG00000122691 HGNC:12428 WDR35 gene WDR35 Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Cranioectodermal dysplasia type 2 (Sensenbrenner syndrome) 613610;613610 24123776 False 3 67;33;0 6.4 True ENSG00000118965 ENSG00000118965 HGNC:29250 ZEB2 gene ZEB2 Expert Review;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Mowat-Wilson syndrome 235730;235730 26097173;25123255;24300291;18076118 False 3 67;33;0 6.4 True ENSG00000169554 ENSG00000169554 HGNC:14881 ZIC1 gene ZIC1 Eligibility statement prior genetic testing;Expert list;Expert Review Green;NHS GMS Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted ?Craniosynostosis 6, 616602;Structural brain anomalies with impaired intellectual development and craniosynostosis, 618736 26340333;27884935;32975022 False 3 67;33;0 6.4 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000152977 ENSG00000152977 HGNC:12872 ZNF462 gene ZNF462 Expert list;Expert Review Green Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Weiss-Kruszka syndrome, OMIM:618619;weiss-kruszka syndrome, MONDO:0032836 28513610;31361404 False 3 100;0;0 6.4 False ENSG00000148143 ENSG00000148143 HGNC:21684 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-37441-Loss region NHS GMS;Expert Review Green;ClinGen Rare syndromic craniosynostosis or isolated multisuture synostosis Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Potocki-Shaffer syndrome;multiple exostoses;biparietal foramina;intellectual disability;strabismus;minor craniofacial anomalies;myopia;ophthalmologic anomalies;601224;mental retardation;enlarged anterior fontanel;genital abnormalities in males;parietal foramina;developmental delay 15852040;16319823;20140962 False 3 100;0;0 6.4 False 11 43873250 46130899 3 60 cnv_loss 11p11.2 (Potocki-Shaffer syndrome) region (includes ALX4, EXT2) Loss 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