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 ALX3 gene ALX3 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal FRONTONASAL DYSPLASIA 1; FND1;Frontorhiny 19409524;22106187;19401770 False 2 0;100;0 6.23 False ENSG00000156150 ENSG00000156150 HGNC:449 ARID1A gene ARID1A Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Coffin-Siris syndrome 2, OMIM:614607 25168959;37010288 False 2 0;100;0 6.23 False ENSG00000117713 ENSG00000117713 HGNC:11110 ARID1B gene ARID1B Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Coffin-Siris syndrome 1, OMIM:135900 30349098;37010288 False 2 0;100;0 6.23 False ENSG00000049618 ENSG00000049618 HGNC:18040 ATR gene ATR Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Seckel syndrome 1, OMIM:210600 False 2 0;100;0 6.23 False ENSG00000175054 ENSG00000175054 HGNC:882 AUTS2 gene AUTS2 Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Intellectual developmental disorder, autosomal dominant 26, OMIM:615834 31788251;37010288 False 2 0;100;0 6.23 False ENSG00000158321 ENSG00000158321 HGNC:14262 B3GALT6 gene B3GALT6 Expert Review Amber Clefting Musculoskeletal SPONDYLOEPIMETAPHYSEAL DYSPLASIA WITH JOINT LAXITY, TYPE 1, WITH OR WITHOUT FRACTURES; SEMDJL1;Ehlers-Danlos syndrome, progeroid type, 2 615349 False 2 0;100;0 6.23 False ENSG00000176022 ENSG00000176022 HGNC:17978 B4GALT7 gene B4GALT7 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal EHLERS-DANLOS SYNDROME WITH SHORT STATURE AND LIMB ANOMALIES; EDSSLA 24755949;26940150;31278392 False 2 0;100;0 6.23 False ENSG00000027847 ENSG00000027847 HGNC:930 BUB1B gene BUB1B Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MOSAIC VARIEGATED ANEUPLOIDY SYNDROME 1; MVA1 False 2 0;100;0 6.23 False ENSG00000156970 ENSG00000156970 HGNC:1149 CDC45 gene CDC45 Expert list;Expert Review Amber;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Meier-Gorlin syndrome 7, 617063;MGORS7 27374770 False 2 0;0;0 6.23 False ENSG00000093009 ENSG00000093009 HGNC:1739 CHD4 gene CHD4 Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Sifrim-Hitz-Weiss syndrome, OMIM:617159 31388190;37010288 False 2 0;100;0 6.23 False ENSG00000111642 ENSG00000111642 HGNC:1919 COL9A2 gene COL9A2 Emory Genetics Laboratory;Expert Review Amber;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Stickler syndrome, type V, OMIM:614284 21671392 False 2 0;100;0 6.23 False ENSG00000049089 ENSG00000049089 HGNC:2218 DDX3X gene DDX3X Expert Review Amber Clefting 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 26235985;27159028;37010288 False 2 0;100;0 6.23 False ENSG00000215301 ENSG00000215301 HGNC:2745 DDX59 gene DDX59 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal OROFACIODIGITAL SYNDROME V; OFD5 False 2 0;100;0 6.23 False ENSG00000118197 ENSG00000118197 HGNC:25360 DLX4 gene DLX4 Expert Review Amber Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ?Orofacial cleft 15, 616788;nonsyndromic cleft/lip palate (CL/P);OROFACIAL CLEFT 15; OFC15 25954033 False 2 0;100;0 6.23 False ENSG00000108813 ENSG00000108813 HGNC:2917 ECEL1 gene ECEL1 Expert Review Amber;Literature Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Arthrogryposis, distal, type 5D, OMIM:615065 30131190;37010288 False 2 0;100;0 6.23 False ENSG00000171551 ENSG00000171551 HGNC:3147 ESRP2 gene ESRP2 Expert list;Expert Review Amber Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown cleft lip 29805042 False 2 0;100;0 6.23 False ENSG00000103067 ENSG00000103067 HGNC:26152 FBXO11 gene FBXO11 Expert list;Expert Review Amber Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown cleft lip;Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities, 618089 30057029;30679813;17035249 False 2 0;100;0 6.23 False ENSG00000138081 ENSG00000138081 HGNC:13590 FGFR3 gene FGFR3 Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Muenke syndrome, OMIM:602849;Hypochondroplasia, OMIM:146000 22565872;29150894;37010288 False 2 0;100;0 6.23 False ENSG00000068078 ENSG00000068078 HGNC:3690 FOXP2 gene FOXP2 Expert list;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Speech-language disorder-1, 602081 27734906;15326624 False 2 0;0;0 6.23 False ENSG00000128573 ENSG00000128573 HGNC:13875 FTO gene FTO Expert list;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Growth retardation, developmental delay, facial dysmorphism, 612938;Lethal polymalformative syndrome, Boissel type 19559399;26378117 False 2 0;0;0 6.23 False ENSG00000140718 ENSG00000140718 HGNC:24678 GATA3 gene GATA3 Expert list;Expert Review Amber;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Hypoparathyroidism, sensorineural deafness, and renal dysplasia, 146255;Barakat syndrome;HDR syndrome 28303854;19659764;10935639;11389161;21834031 False 2 0;0;0 6.23 False ENSG00000107485 ENSG00000107485 HGNC:4172 GNB1 gene GNB1 Expert list;Expert Review Amber;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Mental retardation, autosomal dominant 42 OMIM:616973;intellectual disability, autosomal dominant 42 MONDO:0014855 27108799 False 2 0;0;0 6.23 False Other ENSG00000078369 ENSG00000078369 HGNC:4396 IFT52 gene IFT52 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Short-rib thoracic dysplasia 16 with or without polydactyly, OMIM:617102;Short-rib thoracic dysplasia 16 with or without polydactyly, MONDO:0014915 False 2 0;100;0 6.23 False ENSG00000101052 ENSG00000101052 HGNC:15901 KAT5 gene KAT5 Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Severe global developmental delay;Intellectual disability;Seizures;Microcephaly;Behavioral abnormality;Sleep disturbance;Morphological abnormality of the central nervous system;Short stature;Oral cleft;Abnormality of the face 32822602 False 2 0;100;0 6.23 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000172977 ENSG00000172977 HGNC:5275 KDM1A gene KDM1A Expert Review Amber;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cleft palate,psychomotor retardation,distinctive facial features, 616728 24838796;26656649;23020937 False 2 0;50;50 6.23 False ENSG00000004487 ENSG00000004487 HGNC:29079 KMT2A gene KMT2A Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Wiedemann-Steiner syndrome, OMIM:605130 25929198;30305169;31710778;37010288 False 2 0;100;0 6.23 False ENSG00000118058 ENSG00000118058 HGNC:7132 LMNA gene LMNA Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal RESTRICTIVE DERMOPATHY, LETHAL False 2 0;100;0 6.23 False ENSG00000160789 ENSG00000160789 HGNC:6636 LRRC32 gene LRRC32 Expert Review Amber;Literature Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Cleft palate, proliferative retinopathy, and developmental delay, OMIM:619074 30976112;35656379 False 2 0;100;0 6.23 False ENSG00000137507 ENSG00000137507 HGNC:4161 MED13L gene MED13L Expert Review Amber;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Impaired intellectual development and distinctive facial features with or without cardiac defects, OMIM:616789;MRFACD;Cleft palate 25137640;25712080;29159987;29511999;37010288 False 2 0;100;0 6.23 False ENSG00000123066 ENSG00000123066 HGNC:22962 MEOX1 gene MEOX1 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal KLIPPEL-FEIL SYNDROME 2, AUTOSOMAL RECESSIVE; KFS2 23290072; 24073994 False 2 0;100;0 6.23 False ENSG00000005102 ENSG00000005102 HGNC:7013 NEB gene NEB Expert Review Amber;Literature Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Arthrogryposis multiplex congenita 6, OMIM:619334 12207937;21798101;33376055;37010288 False 2 0;100;0 6.23 False ENSG00000183091 ENSG00000183091 HGNC:7720 NOTCH2 gene NOTCH2 Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Hajdu-Cheney syndrome, OMIM:102500 9188663;30329210;37010288 False 2 0;100;0 6.23 False ENSG00000134250 ENSG00000134250 HGNC:7882 PHGDH gene PHGDH Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal NEU-LAXOVA SYNDROME 1; NLS1 24836451;25152457 False 2 0;100;0 6.23 False ENSG00000092621 ENSG00000092621 HGNC:8923 PLEKHA7 gene PLEKHA7 Expert list;Expert Review Amber Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown cleft lip 29805042 False 2 0;100;0 6.23 False ENSG00000166689 ENSG00000166689 HGNC:27049 POGZ gene POGZ Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted White-Sutton syndrome, OMIM:616364 26739615;31782611;37010288 False 2 0;100;0 6.23 False ENSG00000143442 ENSG00000143442 HGNC:18801 POLR1A gene POLR1A Expert list;Expert Review Amber Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown cleft palte 25913037 False 2 0;100;0 6.23 False ENSG00000068654 ENSG00000068654 HGNC:17264 PRKCI gene PRKCI Expert Review Amber;Other Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown van der Woude syndrome, MONDO:0019508;orofacial cleft, MONDO:0000358 40902599 False 2 100;0;0 6.23 False ENSG00000163558 ENSG00000163558 HGNC:9404 RARB gene RARB Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MICROPHTHALMIA, SYNDROMIC 12; MCOPS12 False 2 0;100;0 6.23 False ENSG00000077092 ENSG00000077092 HGNC:9865 RBPJ gene RBPJ Expert Review Amber Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ADAMS-OLIVER SYNDROME 22883147;28160419 False 2 0;100;0 6.23 False ENSG00000168214 ENSG00000168214 HGNC:5724 RERE gene RERE Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted clefting PMID: 33772547 False 2 0;100;0 6.23 False ENSG00000142599 ENSG00000142599 HGNC:9965 RPS28 gene RPS28 Expert Review Amber;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown DIAMOND-BLACKFAN ANEMIA 15 WITH MANDIBULOFACIAL DYSOSTOSIS;DBA15;Cleft palate False 2 0;100;0 6.23 False ENSG00000233927 ENSG00000233927 HGNC:10418 RYR1 gene RYR1 Expert Review Amber Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal CENTRAL CORE DISEASE OF MUSCLE; CCD 23553484 False 2 0;100;0 6.23 False ENSG00000196218 ENSG00000196218 HGNC:10483 SCUBE3 gene SCUBE3 Expert Review Amber;Other Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies OMIM:619184;short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2 MONDO:0030953 33308444 False 2 50;50;0 6.23 False ENSG00000146197 ENSG00000146197 HGNC:13655 SEC23A gene SEC23A Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal CRANIOLENTICULOSUTURAL DYSPLASIA; CLSD False 2 0;100;0 6.23 False ENSG00000100934 ENSG00000100934 HGNC:10701 SEPT9 gene SEPT9 Expert Review Amber;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown AMYOTROPHY, HEREDITARY NEURALGIC; HNA 11739810;18492087;30019529;31619932;28503616;20019224;19939853;19451530;19139049;16186812 False 2 25;75;0 6.23 False ENSG00000184640 ENSG00000184640 HGNC:7323 SMARCB1 gene SMARCB1 Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Coffin-Siris syndrome 3, OMIM:614608 25168959;37010288 False 2 0;100;0 6.23 False ENSG00000099956 ENSG00000099956 HGNC:11103 SMG9 gene SMG9 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal HEART AND BRAIN MALFORMATION SYNDROME; HBMS 27018474 False 2 0;100;0 6.23 False ENSG00000105771 ENSG00000105771 HGNC:25763 TBL1XR1 gene TBL1XR1 Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Pierpont syndrome, OMIM:602342 28687524;37010288 False 2 0;100;0 6.23 False ENSG00000177565 ENSG00000177565 HGNC:29529 TBX15 gene TBX15 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal COUSIN SYNDROME False 2 0;100;0 6.23 False ENSG00000092607 ENSG00000092607 HGNC:11594 TRAF7 gene TRAF7 Expert Review Amber;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cardiac, facial, and digital anomalies with developmental delay, OMIM:618164 32376980;37010288 False 2 0;100;0 6.23 False ENSG00000131653 ENSG00000131653 HGNC:20456 TTC21B gene TTC21B Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 4 WITH OR WITHOUT POLYDACTYLY; SRTD4 False 2 0;100;0 6.23 False ENSG00000123607 ENSG00000123607 HGNC:25660 UBE3B gene UBE3B Expert Review Amber;Literature Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Kaufman oculocerebrofacial syndrome, OMIM:244450 23200864;23687348;37010288 False 2 0;100;0 6.23 False ENSG00000151148 ENSG00000151148 HGNC:13478 WDR19 gene WDR19 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 5 WITH OR WITHOUT POLYDACTYLY; SRTD5 False 2 0;100;0 6.23 False ENSG00000157796 ENSG00000157796 HGNC:18340 WDR34 gene WDR34 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 11 WITH OR WITHOUT POLYDACTYLY; SRTD11 False 2 0;100;0 6.23 False ENSG00000119333 ENSG00000119333 HGNC:28296 WDR35 gene WDR35 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 7 WITH OR WITHOUT POLYDACTYLY; SRTD7 False 2 0;100;0 6.23 False ENSG00000118965 ENSG00000118965 HGNC:29250 WDR60 gene WDR60 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 8 WITH OR WITHOUT POLYDACTYLY; SRTD8 False 2 0;100;0 6.23 False ENSG00000126870 ENSG00000126870 HGNC:21862 ZBTB24 gene ZBTB24 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal IMMUNODEFICIENCY-CENTROMERIC INSTABILITY-FACIAL ANOMALIES SYNDROME 2; ICF2 23486536 False 2 0;100;0 6.23 False ENSG00000112365 ENSG00000112365 HGNC:21143 ZMPSTE24 gene ZMPSTE24 Expert Review Amber Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal RESTRICTIVE DERMOPATHY, LETHAL False 2 0;100;0 6.23 False ENSG00000084073 ENSG00000084073 HGNC:12877