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 Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown BARAITSER-WINTER SYNDROME 1; BRWS1 22366783 False 3 100;0;0 6.23 False ENSG00000075624 ENSG00000075624 HGNC:132 ACTG1 gene ACTG1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown BARAITSER-WINTER SYNDROME 2; BRWS2 22366783 False 3 100;0;0 6.23 False ENSG00000184009 ENSG00000184009 HGNC:144 ALX1 gene ALX1 Expert list;Expert Review Green;NHS GMS Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Frontonasal dysplasia 3, OMIM:613456;frontonasal dysplasia - severe microphthalmia - severe facial clefting syndrome, MONDO:0013271 20451171;27324866;26610632;23059813;32914578 False 3 50;50;0 6.23 False ENSG00000180318 ENSG00000180318 HGNC:1494 AMER1 gene AMER1 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) OSTEOPATHIA STRIATA WITH CRANIAL SCLEROSIS;OSCS;Cleft palate False 3 100;0;0 6.23 False ENSG00000184675 ENSG00000184675 HGNC:26837 AMOTL1 gene AMOTL1 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Craniofaciocardiohepatic syndrome, OMIM:621192;craniofaciocardiohepatic syndrome, MONDO:0978295 30375152;33026150;36751037 False 3 50;0;50 6.23 False ENSG00000166025 ENSG00000166025 HGNC:17811 ANKRD11 gene ANKRD11 Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted KBG syndrome,148050 (orofacial clefting, intellectual disability, dental anomalies, dysmorphism);Short stature-facial and skeletal anomalies-intellectual disability-macrodontia syndrome;Orofacial Clefting with skeletal features 21782149;25838844;2705097;27900361 False 3 0;0;0 6.23 False ENSG00000167522 ENSG00000167522 HGNC:21316 ARHGAP29 gene ARHGAP29 Expert Review Green;Research;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted cleft lip with or without cleft palate;Cleft palate 23008150;25704602;27350171;27369588;27033726;25512736;27350171;28029220;27033726 False 3 100;0;0 6.23 False ENSG00000137962 ENSG00000137962 HGNC:30207 ARHGAP31 gene ARHGAP31 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ADAMS-OLIVER SYNDROME 1; AOS1 False 3 100;0;0 6.23 False ENSG00000031081 ENSG00000031081 HGNC:29216 ASXL1 gene ASXL1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Bohring-Opitz syndrome, OMIM:605039;Bohring-Opitz syndrome, MONDO:0011510 False 3 100;0;0 6.23 False ENSG00000171456 ENSG00000171456 HGNC:18318 B3GLCT gene B3GLCT Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal PETERS-PLUS SYNDROME False 3 100;0;0 6.23 False ENSG00000187676 ENSG00000187676 HGNC:20207 BCOR gene BCOR Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) MICROPHTHALMIA, SYNDROMIC 2; MCOPS2 False 3 100;0;0 6.23 False ENSG00000183337 ENSG00000183337 HGNC:20893 BMP2 gene BMP2 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cleft palate;Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies, 617877 21671386;29198724 False 3 100;0;0 6.23 False ENSG00000125845 ENSG00000125845 HGNC:1069 C2CD3 gene C2CD3 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal OROFACIODIGITAL SYNDROME XIV; OFD14 False 3 100;0;0 6.23 False ENSG00000168014 ENSG00000168014 HGNC:24564 C5orf42 gene C5orf42 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal OROFACIODIGITAL SYNDROME VI; OFD6 False 3 100;0;0 6.23 False ENSG00000197603 ENSG00000197603 HGNC:25801 CC2D2A gene CC2D2A Expert list;Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Meckel syndrome 6, 612284;MKS6;Meckel-Gruber syndrome 18513680;19777577 False 3 0;0;0 6.23 False ENSG00000048342 ENSG00000048342 HGNC:29253 CDH1 gene CDH1 Expert Review Green;Other Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Blepharocheilodontic syndrome 1, OMIM:119580;Diffuse gastric and lobular breast cancer syndrome with or without cleft lip and/or palate, OMIM:137215 28301459;27566442 False 3 100;0;0 6.23 False ENSG00000039068 ENSG00000039068 HGNC:1748 CDKN1C gene CDKN1C Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed) BECKWITH-WIEDEMANN SYNDROME; BWS 20503313 False 3 100;0;0 6.23 False ENSG00000129757 ENSG00000129757 HGNC:1786 CHD7 gene CHD7 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown CHARGE SYNDROME False 3 100;0;0 6.23 False ENSG00000171316 ENSG00000171316 HGNC:20626 CHRNG gene CHRNG Expert list;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Escobar syndrome, 265000;MULTIPLE PTERYGIUM SYNDROME, NONLETHAL TYPE;Multiple pterygium syndrome, lethal type, 253290;PTERYGIUM SYNDROME, MULTIPLE, LETHAL TYPE 16826520;22167768;27843868 False 3 0;0;0 6.23 False ENSG00000196811 ENSG00000196811 HGNC:1967 CHST14 gene CHST14 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal EHLERS-DANLOS SYNDROME, MUSCULOCONTRACTURAL TYPE, 1; EDSMC1 False 3 100;0;0 6.23 False ENSG00000169105 ENSG00000169105 HGNC:24464 CNTNAP1 gene CNTNAP1 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Hypomyelinating neuropathy, congenital, 3, OMIM:618186 28374019;29511323;29882456;37010288 False 3 100;0;0 6.23 False ENSG00000108797 ENSG00000108797 HGNC:8011 COL11A1 gene COL11A1 Eligibility statement prior genetic testing;Expert Review Green;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Marshall Syndrome, OMIM:154780;Stickler syndrome, type II, OMIM:604841 False 3 100;0;0 6.23 False ENSG00000060718 ENSG00000060718 HGNC:2186 COL11A2 gene COL11A2 Eligibility statement prior genetic testing;Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Stickler syndrome, type III;STICKLER SYNDROME, NONOCULAR TYPE;OSMED;STL3;Non-ocular Stickler syndrome;Cleft palate False 3 100;0;0 6.23 False ENSG00000204248 ENSG00000204248 HGNC:2187 COL2A1 gene COL2A1 Eligibility statement prior genetic testing;Expert Review Green;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal STICKLER SYNDROME, TYPE I (STL1), 108300;Orofacial Clefting with skeletal features;Stickler Syndrome;Stickler syndrome (cleft palate,micrognathia,vireo-retinal anomalies, severe myopia, joint problems, hearing loss);Stickler sydrome, type I, non syndromic ocular;STICKLER SYNDROME, VITREOUS TYPE 1;STICKLER SYNDROME, MEMBRANOUS VITREOUS TYPE;ARTHROOPHTHALMOPATHY, HEREDITARY PROGRESSIVE, AOM;STICKLER SYNDROME, TYPE I;STL1;Cleft palate 16752401;17721977;1677770 False 3 100;0;0 6.23 False ENSG00000139219 ENSG00000139219 HGNC:2200 COL9A1 gene COL9A1 Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Stickler syndrome, type IV, OMIM:614134 16909383;21421862 False 3 100;0;0 6.23 False ENSG00000112280 ENSG00000112280 HGNC:2217 COLEC10 gene COLEC10 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 3MC SYNDROME 3; 3MC3 21258343 False 3 100;0;0 6.23 False ENSG00000184374 ENSG00000184374 HGNC:2220 COLEC11 gene COLEC11 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 3MC SYNDROME 2; 3MC2 False 3 100;0;0 6.23 False ENSG00000118004 ENSG00000118004 HGNC:17213 CTCF gene CTCF Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown MENTAL RETARDATION, AUTOSOMAL DOMINANT 21; MRD21 False 3 100;0;0 6.23 False ENSG00000102974 ENSG00000102974 HGNC:13723 CTGF gene CTGF Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Kyphomelic dysplasia, OMIM:211350;kyphomelic dysplasia, MONDO:0008881;spondyloepimetaphyseal dysplasia, MONDO:0100510 39506047;39414788;12736220 False 3 100;0;0 6.23 False ENSG00000118523 ENSG00000118523 HGNC:2500 CTNND1 gene CTNND1 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown BLEPHAROCHEILODONTIC;Cleft palate 28301459;32196547 False 3 100;0;0 6.23 False ENSG00000198561 ENSG00000198561 HGNC:2515 DHCR7 gene DHCR7 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SMITH-LEMLI-OPITZ SYNDROME; SLOS False 3 100;0;0 6.23 False ENSG00000172893 ENSG00000172893 HGNC:2860 DHODH gene DHODH Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal POSTAXIAL ACROFACIAL DYSOSTOSIS; POADS = MILLER False 3 100;0;0 6.23 False ENSG00000102967 ENSG00000102967 HGNC:2867 DLL4 gene DLL4 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ADAMS-OLIVER SYNDROME False 3 100;0;0 6.23 False ENSG00000128917 ENSG00000128917 HGNC:2910 DOCK6 gene DOCK6 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal ADAMS-OLIVER SYNDROME False 3 100;0;0 6.23 False ENSG00000130158 ENSG00000130158 HGNC:19189 DVL1 gene DVL1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ROBINOW SYNDROME, AUTOSOMAL DOMINANT 2; DRS2 False 3 100;0;0 6.23 False ENSG00000107404 ENSG00000107404 HGNC:3084 DVL3 gene DVL3 Expert Review Green;Other Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Robinow syndrome, autosomal dominant 3, 616894 26924530;29575616 False 3 100;0;0 6.23 False ENSG00000161202 ENSG00000161202 HGNC:3087 DYNC2H1 gene DYNC2H1 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Short-rib thoracic dysplasia 3 with or without polydactyly, OMIM:613091 False 3 100;0;0 6.23 False ENSG00000187240 ENSG00000187240 HGNC:2962 DYNC2LI1 gene DYNC2LI1 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 15 WITH POLYDACTYLY; SRTD15 False 3 100;0;0 6.23 False ENSG00000138036 ENSG00000138036 HGNC:24595 EBP gene EBP Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females MEND SYNDROME; MEND False 3 100;0;0 6.23 False ENSG00000147155 ENSG00000147155 HGNC:3133 EDNRA gene EDNRA Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown MANDIBULOFACIAL DYSOSTOSIS WITH ALOPECIA;MFDA;Cleft palate False 3 100;0;0 6.23 False ENSG00000151617 ENSG00000151617 HGNC:3179 EFNB1 gene EFNB1 Expert Review Green Clefting 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 False 3 100;0;0 6.23 False ENSG00000090776 ENSG00000090776 HGNC:3226 EFTUD2 gene EFTUD2 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown MANDIBULOFACIAL DYSOSTOSIS, GUION-ALMEIDA TYPE; MFDGA False 3 100;0;0 6.23 False ENSG00000108883 ENSG00000108883 HGNC:30858 EIF2S3 gene EIF2S3 Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females MENTAL RETARDATION, X-LINKED, SYNDROMIC, BORCK TYPE; MRXSBRK False 3 100;0;0 6.23 False ENSG00000130741 ENSG00000130741 HGNC:3267 EIF4A3 gene EIF4A3 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Cleft palate;Robin sequence with cleft mandible and limb anomalies, 268305;Richieri-Costa-Pereira syndrome 10594883;29922329;29112243 False 3 100;0;0 6.23 False ENSG00000141543 ENSG00000141543 HGNC:18683 EOGT gene EOGT Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal ADAMS-OLIVER SYNDROME False 3 100;0;0 6.23 False ENSG00000163378 ENSG00000163378 HGNC:28526 EPG5 gene EPG5 Expert list;Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Vici syndrome, 242840 3344762;23222957;17163544;20583151;26927810 False 3 100;0;0 6.23 False ENSG00000152223 ENSG00000152223 HGNC:29331 ESCO2 gene ESCO2 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Roberts-SC phocomelia syndrome, OMIM:268300;Roberts-SC phocomelia syndrome, MONDO:0100253 32977150;32255174;15821733;16380922;18411254;24864645 False 3 100;0;0 6.23 False ENSG00000171320 ENSG00000171320 HGNC:27230 EYA1 gene EYA1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted BRANCHIOOTORENAL SYNDROME 1; BOR1 False 3 100;0;0 6.23 False ENSG00000104313 ENSG00000104313 HGNC:3519 FAM20C gene FAM20C Emory Genetics Laboratory;Expert list;Expert Review Green;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Raine syndrome, 259775 2614802;10482879;17924334;25974638;2194867118000911 False 3 0;0;0 6.23 False ENSG00000177706 ENSG00000177706 HGNC:22140 FGD1 gene FGD1 Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females AARSKOG-SCOTT SYNDROME; AAS 20082460 False 3 100;0;0 6.23 False ENSG00000102302 ENSG00000102302 HGNC:3663 FGFR1 gene FGFR1 Emory Genetics Laboratory;Expert list;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Hartsfield syndrome, 615465;Hypogonadotropic hypogonadism 2 with or without anosmia, 147950;Kallmann syndrome 2 1342859;14564207;19504604;12627230;12627230;16606836;25394172 False 3 100;0;0 6.23 False ENSG00000077782 ENSG00000077782 HGNC:3688 FGFR2 gene FGFR2 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown APERT SYNDROME False 3 100;0;0 6.23 False ENSG00000066468 ENSG00000066468 HGNC:3689 FLNA gene FLNA Expert Review Green;UKGTN Clefting 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 10706363;20301567;16538226;12612583 False 3 100;0;0 6.23 False ENSG00000196924 ENSG00000196924 HGNC:3754 FLNB gene FLNB Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Skeletal dysplasia with midline cleft palate;Orofacial Clefting with skeletal features;Spondylocarpotarsal synostosis syndrome (includes clefting), BIALLELIC, autosomal or pseudoautosomal, 272460;Larsen syndrome (includes clefting) MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown, 150250;Atelosteogenesis, type I (includes clefting), MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown, 108720;Atelosteogenesis, type III MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown (includes clefting), 108721 False 3 0;0;0 6.23 False ENSG00000136068 ENSG00000136068 HGNC:3755 FOXC2 gene FOXC2 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown LYMPHEDEMA-DISTICHIASIS SYNDROME;Cleft palate False 3 100;0;0 6.23 False ENSG00000176692 ENSG00000176692 HGNC:3801 FRAS1 gene FRAS1 Expert list;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Fraser syndrome, 219000 16894541;18671281;16894541;17163535;18203166 False 3 0;0;0 6.23 False ENSG00000138759 ENSG00000138759 HGNC:19185 GDF11 gene GDF11 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Vertebral hypersegmentation and orofacial anomalies (VHO), OMIM:619122 31215115;34113007;10391213;34061439 False 3 100;0;0 6.23 False ENSG00000135414 ENSG00000135414 HGNC:4216 GJA1 gene GJA1 Expert list;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Oculodentodigital dysplasia, OMIM:164200 19338053;12457340;15108203;1057461 False 3 0;0;0 6.23 False ENSG00000152661 ENSG00000152661 HGNC:4274 GLI2 gene GLI2 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Culler-Jones syndrome, OMIM:615849;Holoprosencephaly 9, OMIM:610829 24744436;37010288 False 3 100;0;0 6.23 False ENSG00000074047 ENSG00000074047 HGNC:4318 GLI3 gene GLI3 Expert list;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Pallister-Hall syndrome, OMIM:146510 7211952;1605268;15739154;24736735;20301638 False 3 0;0;0 6.23 False ENSG00000106571 ENSG00000106571 HGNC:4319 GPC3 gene GPC3 Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) SIMPSON-GOLABI-BEHMEL SYNDROME, TYPE 1; SGBS1 False 3 100;0;0 6.23 False ENSG00000147257 ENSG00000147257 HGNC:4451 GRHL3 gene GRHL3 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown VAN DER WOUDE SYNDROME 2;Cleft lip False 3 100;0;0 6.23 False ENSG00000158055 ENSG00000158055 HGNC:25839 HDAC8 gene HDAC8 Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) CORNELIA DE LANGE SYNDROME 5; CDLS5 False 3 100;0;0 6.23 False ENSG00000147099 ENSG00000147099 HGNC:13315 HNRNPK gene HNRNPK Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Au-Kline syndrome, OMIM:616580 29904177;37010288 False 3 100;0;0 6.23 False ENSG00000165119 ENSG00000165119 HGNC:5044 HYAL2 gene HYAL2 Expert Review Green;Literature Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Muggenthaler-Chowdhury-Chioza syndrome, OMIM:621063 28081210 False 3 50;0;50 6.23 False ENSG00000068001 ENSG00000068001 HGNC:5321 HYLS1 gene HYLS1 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Hydrolethalus syndrome, 236680 (includes Cleft palate, Lateral or midline cleft lip, Lower lip cleft) 3296755; 8322817; 22029171; 15843405 False 3 100;0;0 6.23 False ENSG00000198331 ENSG00000198331 HGNC:26558 ICK gene ICK Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Endocrine-cerebroosteodysplasia, OMIM:612651;Endocrine-cerebro-osteodysplasia syndrome, MONDO:0012980 19185282; 24853502; 27069622 False 3 100;0;0 6.23 False ENSG00000112144 ENSG00000112144 HGNC:21219 IFT140 gene IFT140 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 9 WITH OR WITHOUT POLYDACTYLY; SRTD9 False 3 100;0;0 6.23 False ENSG00000187535 ENSG00000187535 HGNC:29077 IFT172 gene IFT172 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 10 WITH OR WITHOUT POLYDACTYLY; SRTD10 False 3 100;0;0 6.23 False ENSG00000138002 ENSG00000138002 HGNC:30391 IFT80 gene IFT80 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 2 WITH OR WITHOUT POLYDACTYLY; SRTD2 False 3 100;0;0 6.23 False ENSG00000068885 ENSG00000068885 HGNC:29262 IMPAD1 gene IMPAD1 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Chondrodysplasia with joint dislocations, GPAPP type, 614078 (includes cleft palate) 21549340; 22887726 False 3 100;0;0 6.23 False ENSG00000104331 ENSG00000104331 HGNC:26019 IRF6 gene IRF6 Eligibility statement prior genetic testing;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Orofacial cleft 6, 608864;Cleft Lip with or without Cleft Palate;Orofacial Clefting with skeletal features;Cleft lip +/- palate- unilateral or bilateral;cleft palate;lip pits;VAN DER WOUDE SYNDROME 1;VWS1, POPLITEAL PTERYGIUM SYNDROME;PPS;Cleft palate False 3 100;0;0 6.23 False ENSG00000117595 ENSG00000117595 HGNC:6121 KAT6A gene KAT6A Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown MENTAL RETARDATION, AUTOSOMAL DOMINANT 32; MRD32 False 3 100;0;0 6.23 False ENSG00000083168 ENSG00000083168 HGNC:13013 KAT6B gene KAT6B Expert Review Green;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Genitopatellar syndrome, OMIM:606170;SBBYSS syndrome, OMIM:603736 20182757;27031267;32424177;37010288 False 3 33;33;33 6.23 False ENSG00000156650 ENSG00000156650 HGNC:17582 KCNJ2 gene KCNJ2 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Andersen syndrome, OMIM:170390;Andersen-Tawil syndrome, MONDO:0008222 12163457 False 3 100;0;0 6.23 False ENSG00000123700 ENSG00000123700 HGNC:6263 KDM6A gene KDM6A Emory Genetics Laboratory;Expert Review;Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Kabuki syndrome 2, 300867 22197486;23076834;24664873 False 3 100;0;0 6.23 False ENSG00000147050 ENSG00000147050 HGNC:12637 KIAA0586 gene KIAA0586 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 14 WITH POLYDACTYLY; SRTD14 False 3 100;0;0 6.23 False ENSG00000100578 ENSG00000100578 HGNC:19960 KIF1BP gene KIF1BP Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Goldberg-Shprintzen megacolon syndrome, 609460; GOSHS 16760737; 7338549 False 3 100;0;0 6.23 False ENSG00000198954 ENSG00000198954 HGNC:23419 KIF7 gene KIF7 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal ACROCALLOSAL SYNDROME; ACLS 21552264 False 3 100;0;0 6.23 False ENSG00000166813 ENSG00000166813 HGNC:30497 KMT2D gene KMT2D Emory Genetics Laboratory;Expert Review;Expert Review Green;Literature;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Kabuki syndrome 1, 147920 20711175;21671394;22126750;26049589;25142838 False 3 100;0;0 6.23 False ENSG00000167548 ENSG00000167548 HGNC:7133 MAP3K7 gene MAP3K7 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Frontometaphyseal dysplasia 2, 617137; FMD2; autosomal dominant FMD; AD-FMD 28498505; 25899317 False 3 100;0;0 6.23 False ENSG00000135341 ENSG00000135341 HGNC:6859 MAPRE2 gene MAPRE2 Expert list;Expert Review Green Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Symmetric circumferential skin creases, congenital, 2, 616734 26637975 False 3 100;0;0 6.23 False ENSG00000166974 ENSG00000166974 HGNC:6891 MASP1 gene MASP1 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 3MC SYNDROME 1; 3MC1 False 3 100;0;0 6.23 False ENSG00000127241 ENSG00000127241 HGNC:6901 MBTPS2 gene MBTPS2 Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females IFAP SYNDROME WITH OR WITHOUT BRESHECK SYNDROME False 3 100;0;0 6.23 False ENSG00000012174 ENSG00000012174 HGNC:15455 MED12 gene MED12 Expert Review Green;NHS GMS Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Hardikar syndrome, OMIM:612726;cholestasis-pigmentary retinopathy-cleft palate syndrome, MONDO:0012997 33244166 False 3 75;0;25 6.23 False ENSG00000184634 ENSG00000184634 HGNC:11957 MED16 gene MED16 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Guillouet-Gordon syndrome, OMIM:621220 40081376 False 3 100;0;0 6.23 False ENSG00000175221 ENSG00000175221 HGNC:17556 MED25 gene MED25 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Basel-Vanagait-Smirin-Yosef syndrome OMIM:616449 25792360;31602195;32324310;32816121 False 3 0;100;0 6.23 False ENSG00000104973 ENSG00000104973 HGNC:28845 MEIS2 gene MEIS2 Expert Review;Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cleft palate, cardiac defects, and mental retardation, OMIM:600987;Cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies, MONDO:0010970 25712757;27225850;24678003 False 3 100;0;0 6.23 False ENSG00000134138 ENSG00000134138 HGNC:7001 MID1 gene MID1 Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) OPITZ GBBB SYNDROME, TYPE I; GBBB1 False 3 100;0;0 6.23 False ENSG00000101871 ENSG00000101871 HGNC:7095 MKS1 gene MKS1 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Meckel syndrome 1, 249000; MKS1; Meckel-Gruber Syndrome (MGS) 26037304; 25182137; 24643152 False 3 100;0;0 6.23 False ENSG00000011143 ENSG00000011143 HGNC:7121 MSX1 gene MSX1 Expert Review Green;Radboud University Medical Center, Nijmegen;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Orofacial cleft 5, OMIM:608874;Tooth agenesis, selective, 1, with or without orofacial cleft, OMIM:106600 10742093;12807959;27228008;12097313;16498076;15264286;25565750 False 3 100;0;0 6.23 False ENSG00000163132 ENSG00000163132 HGNC:7391 MYMK gene MYMK Expert Review Green;Literature Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Carey-Fineman-Ziter syndrome, OMIM:254940;Carey-Fineman-Ziter syndrome, MONDO:0009700 28681861 False 3 100;0;0 6.23 False ENSG00000187616 ENSG00000187616 HGNC:33778 NECTIN1 gene NECTIN1 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Cleft lip/Palate ectodermal dysplasia syndrome, 225060;Orofacial cleft 7, 225060;Cleft Lip with or without Cleft Palate;Zlotogora-Ogur syndrome;CLP, partial syndactyly of digits, intellectual disability, dysmorphism;Ectodermal dysplasia, Margarita Island type;Cleft lip 26953873;11559849;10932188 False 3 100;0;0 6.23 False ENSG00000110400 ENSG00000110400 HGNC:9706 NEDD4L gene NEDD4L Expert Review;Expert Review Green;Literature;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cleft palate, toe syndactyly, periventricular nodular heterotopia;Periventricular nodular heterotopia 7 (includes clefting), 617201;Cleft palate 27694961 False 3 100;0;0 6.23 False ENSG00000049759 ENSG00000049759 HGNC:7728 NEK1 gene NEK1 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal SHORT-RIB THORACIC DYSPLASIA 6 WITH OR WITHOUT POLYDACTYLY; SRTD6 False 3 100;0;0 6.23 False ENSG00000137601 ENSG00000137601 HGNC:7744 NIPBL gene NIPBL Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown CORNELIA DE LANGE SYNDROME 1; CDLS1 False 3 100;0;0 6.23 False ENSG00000164190 ENSG00000164190 HGNC:28862 NOTCH1 gene NOTCH1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ADAMS-OLIVER SYNDROME False 3 100;0;0 6.23 False ENSG00000148400 ENSG00000148400 HGNC:7881 OFD1 gene OFD1 Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) OROFACIODIGITAL SYNDROME I; OFD1 False 3 100;0;0 6.23 False ENSG00000046651 ENSG00000046651 HGNC:2567 PAX3 gene PAX3 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown WAARDENBURG False 3 100;0;0 6.23 False ENSG00000135903 ENSG00000135903 HGNC:8617 PGAP3 gene PGAP3 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Hyperphosphatasia with impaired intellectual development syndrome 4, OMIM:615716 28390064;37010288 False 3 100;0;0 6.23 False ENSG00000161395 ENSG00000161395 HGNC:23719 PGM1 gene PGM1 Expert Review Green;NHS GMS;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Congenital disorder of glycosylation, type It, OMIM:14921 24499211;37010288 False 3 100;0;0 6.23 False ENSG00000079739 ENSG00000079739 HGNC:8905 PHF8 gene PHF8 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females SIDERIUS X-LINKED MENTAL RETARDATION SYNDROME;MRXSSD;Cleft lip False 3 100;0;0 6.23 False ENSG00000172943 ENSG00000172943 HGNC:20672 PIEZO2 gene PIEZO2 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ARTHROGRYPOSIS, DISTAL, TYPE 3; DA3, MARDEN-WALKER SYNDROME; MWKS 24726473 False 3 100;0;0 6.23 False ENSG00000154864 ENSG00000154864 HGNC:26270 PIGN gene PIGN Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 1; MCAHS1 24852103;27038415 False 3 100;0;0 6.23 False ENSG00000197563 ENSG00000197563 HGNC:8967 PIGV gene PIGV Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 1; HPMRS1 21739589;24129430 False 3 100;0;0 6.23 False ENSG00000060642 ENSG00000060642 HGNC:26031 PLCB4 gene PLCB4 Expert Review Green;NHS GMS;Victorian Clinical Genetics Services Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Auriculocondylar syndrome 2, OMIM:614669;auriculocondylar syndrome 2, MONDO:0013845 16114046;32201334;27007857;23913798;22560091;23315542 False 3 100;0;0 6.23 False ENSG00000101333 ENSG00000101333 HGNC:9059 POLR1B gene POLR1B Expert Review Green;Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Treacher-Collins syndrome 4 OMIM:618939;treacher collins syndrome 4 MONDO:0030067 31649276 False 3 100;0;0 6.23 False ENSG00000125630 ENSG00000125630 HGNC:20454 POLR1C gene POLR1C Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal TREACHER COLLINS SYNDROME 3; TCS3 False 3 100;0;0 6.23 False ENSG00000171453 ENSG00000171453 HGNC:20194 POLR1D gene POLR1D Expert Review Green Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Treacher Collins syndrome 2, OMIM:613717 False 3 100;0;0 6.23 False ENSG00000186184 ENSG00000186184 HGNC:20422 PORCN gene PORCN Emory Genetics Laboratory;Expert list;Expert Review Green;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Focal dermal hypoplasia, 305600;GOLTZ SYNDROME 12071796;18325042;20301712;10602117;21484999;13948891 False 3 0;0;0 6.23 False ENSG00000102312 ENSG00000102312 HGNC:17652 PTCH1 gene PTCH1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 7, OMIM:610828;Basal cell nevus syndrome 1, OMIM:109400 False 3 100;0;0 6.23 False ENSG00000185920 ENSG00000185920 HGNC:9585 RAD21 gene RAD21 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cornelia de Lange syndrome 4, OMIM:614701 22633399;27882533;31334757;32193685 False 3 100;0;0 6.23 False ENSG00000164754 ENSG00000164754 HGNC:9811 RBM10 gene RBM10 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females TARP SYNDROME;TARPS;Cleft palate 20451169 False 3 100;0;0 6.23 False ENSG00000182872 ENSG00000182872 HGNC:9896 ROR2 gene ROR2 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Robinow syndrome, autosomal recessive, OMIM:268310 False 3 100;0;0 6.23 False ENSG00000169071 ENSG00000169071 HGNC:10257 RPL5 gene RPL5 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown DIAMOND-BLACKFAN ANEMIA 6;DBA6;Cleft palate 19061985 False 3 100;0;0 6.23 False ENSG00000122406 ENSG00000122406 HGNC:10360 RPS26 gene RPS26 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown DIAMOND-BLACKFAN ANEMIA 10;DBA10;Cleft palate 20116044 False 3 100;0;0 6.23 False ENSG00000197728 ENSG00000197728 HGNC:10414 SALL4 gene SALL4 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown DUANE-RADIAL RAY SYNDROME; DRRS False 3 100;0;0 6.23 False ENSG00000101115 ENSG00000101115 HGNC:15924 SATB2 gene SATB2 Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Glass syndrome;Chromosome 2q32-q33 deletion syndrome;Orofacial Clefting with skeletal features;Cleft palate, intellectual disability, poor- absent speech, bone fragility- raised serum alkaline phosphatas;GLASS SYNDROME;GLASS;Cleft palate 16179223 False 3 100;0;0 6.23 False ENSG00000119042 ENSG00000119042 HGNC:21637 SCARF2 gene SCARF2 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal VAN DEN ENDE-GUPTA SYNDROME; VDEGS False 3 100;0;0 6.23 False ENSG00000244486 ENSG00000244486 HGNC:19869 SF3B2 gene SF3B2 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Craniofacial microsomia 34344887 False 3 100;0;0 6.23 False ENSG00000087365 ENSG00000087365 HGNC:10769 SF3B4 gene SF3B4 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ACROFACIAL DYSOSTOSIS 1, NAGER TYPE; AFD1 22541558 False 3 100;0;0 6.23 False ENSG00000143368 ENSG00000143368 HGNC:10771 SHH gene SHH Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown HOLOPROSENCEPHALY 3; HPE3 False 3 100;0;0 6.23 False ENSG00000164690 ENSG00000164690 HGNC:10848 SIX1 gene SIX1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown BRANCHIOOTIC SYNDROME 3; BOS3 False 3 100;0;0 6.23 False ENSG00000126778 ENSG00000126778 HGNC:10887 SIX3 gene SIX3 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown HOLOPROSENCEPHALY 2; HPE2 False 3 100;0;0 6.23 False ENSG00000138083 ENSG00000138083 HGNC:10889 SKI gene SKI Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown SHPRINTZEN-GOLDBERG CRANIOSYNOSTOSIS SYNDROME; SGS False 3 100;0;0 6.23 False ENSG00000157933 ENSG00000157933 HGNC:10896 SLC26A2 gene SLC26A2 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Orofacial Clefting with skeletal features;Atelosteogenesis II (includes clefting), 256050;De la Chapelle dysplasia (includes clefting), 256050;McAlister Dysplasia;Diastrophic dysplasia (includes clefting), 222600;Diastrophic dysplasia, broad bonehplatyspondylic variant, 222600;DIASTROPHIC DYSPLASIA; DTD 18708426;8571951;15316973;8931695;7923357;15316973;18708426;10465113;11565064;12866518;25667404 False 3 50;0;50 6.23 False ENSG00000155850 ENSG00000155850 HGNC:10994 SMAD3 gene SMAD3 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown LOEYS-DIETZ SYNDROME 3; LDS3 False 3 100;0;0 6.23 False ENSG00000166949 ENSG00000166949 HGNC:6769 SMAD4 gene SMAD4 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown MYHRE SYNDROME; MYHRS False 3 100;0;0 6.23 False ENSG00000141646 ENSG00000141646 HGNC:6770 SMARCA4 gene SMARCA4 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Coffin-Siris syndrome 4, OMIM:614609 25168959;37010288 False 3 100;0;0 6.23 False ENSG00000127616 ENSG00000127616 HGNC:11100 SMC1A gene SMC1A Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Cornelia de Lange syndrome 2, OMIM:300590;Cornelia de Lange syndrome 2, MONDO:0010370;Developmental and epileptic encephalopathy 85, with or without midline brain defects, OMIM:301044;Developmental and epileptic encephalopathy, 85, with or without midline brain defects, MONDO:0026771 False 3 100;0;0 6.23 False ENSG00000072501 ENSG00000072501 HGNC:11111 SMC3 gene SMC3 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown CORNELIA DE LANGE SYNDROME 3; CDLS3 False 3 100;0;0 6.23 False ENSG00000108055 ENSG00000108055 HGNC:2468 SMS gene SMS Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females MENTAL RETARDATION, X-LINKED, SYNDROMIC, SNYDER-ROBINSON TYPE; MRXSSR False 3 100;0;0 6.23 False ENSG00000102172 ENSG00000102172 HGNC:11123 SNRPB gene SNRPB Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown CEREBROCOSTOMANDIBULAR SYNDROME;CCMS;Cleft palate 25047197 False 3 100;0;0 6.23 False ENSG00000125835 ENSG00000125835 HGNC:11153 SON gene SON Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ZTTK SYNDROME; ZTTKS 27545680 False 3 100;0;0 6.23 False ENSG00000159140 ENSG00000159140 HGNC:11183 SOX9 gene SOX9 Emory Genetics Laboratory;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Orofacial Clefting with Skeletal Features;Cleft palate with skeletal abnormalities;CAMPOMELIC DYSPLASIA,114290;Acampomelic campomelic dysplasia, 114290;Campomelic dysplasia with autosomal sex reversal, 114290;CAMPOMELIC DYSPLASIA;Cleft palate 7990924;8894698;15806394;24038782;7485151;19449405;12783851 False 3 100;0;0 6.23 False ENSG00000125398 ENSG00000125398 HGNC:11204 SPECC1L gene SPECC1L Expert Review Green;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ?Facial clefting, oblique, 1, 600251;Opitz GBBB syndrome, type II (with clefting), 145410;OPITZ GBBB SYNDROME, TYPE II; GBBB2 1897571;8849002;21703590;25412741 False 3 100;0;0 6.23 False ENSG00000100014 ENSG00000100014 HGNC:29022 STAG2 gene STAG2 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Holoprosencephaly 13, X-linked, OMIM:301043;Mullegama-Klein-Martinez syndrome, OMIM:301022 28296084;29263825;30158690;31334757;33014403;37010288 False 3 100;0;0 6.23 False ENSG00000101972 ENSG00000101972 HGNC:11355 STAMBP gene STAMBP Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Microcephaly-capillary malformation syndrome, OMIM:614261 False 3 100;0;0 6.23 False ENSG00000124356 ENSG00000124356 HGNC:16950 TBX1 gene TBX1 Expert Review Green;NHS GMS;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown DiGeorge syndrome, OMIM:188400;Conotruncal anomaly face syndrome, OMIM:217095;Velocardiofacial syndrome, OMIM:192430 14585638;17273972;30137364 False 3 67;33;0 6.23 False ENSG00000184058 ENSG00000184058 HGNC:11592 TBX22 gene TBX22 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;Victorian Clinical Genetics Services Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Cleft palate with ankyloglossia, 303400;sub mucous cleft;palate;cleft lip;CLEFT PALATE WITH OR WITHOUT ANKYLOGLOSSIA, X-LINKED;CPX;Cleft palate 11559848;12374769;14729838;17846996;19648124;19648291;21248356;22784330 False 3 100;0;0 6.23 False ENSG00000122145 ENSG00000122145 HGNC:11600 TCOF1 gene TCOF1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted TREACHER COLLINS SYNDROME 1; TCS1 False 3 100;0;0 6.23 False ENSG00000070814 ENSG00000070814 HGNC:11654 TCTN3 gene TCTN3 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal OROFACIODIGITAL SYNDROME IV; OFD4 False 3 100;0;0 6.23 False ENSG00000119977 ENSG00000119977 HGNC:24519 TELO2 gene TELO2 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal YOU-HOOVER-FONG SYNDROME; YHFS False 3 100;0;0 6.23 False ENSG00000100726 ENSG00000100726 HGNC:29099 TFAP2A gene TFAP2A Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown BRANCHIOOCULOFACIAL SYNDROME;BOFS;Cleft lip 10767004 False 3 100;0;0 6.23 False ENSG00000137203 ENSG00000137203 HGNC:11742 TGDS gene TGDS Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal CATEL-MANZKE SYNDROME;CATMANS;Cleft palate 25480037 False 3 100;0;0 6.23 False ENSG00000088451 ENSG00000088451 HGNC:20324 TGFB3 gene TGFB3 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown LOEYS-DIETZ SYNDROME 5; LDS5 False 3 100;0;0 6.23 False ENSG00000119699 ENSG00000119699 HGNC:11769 TGFBR1 gene TGFBR1 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown LOEYS-DIETZ SYNDROME 1; LDS1 False 3 100;0;0 6.23 False ENSG00000106799 ENSG00000106799 HGNC:11772 TGFBR2 gene TGFBR2 Expert Review;Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Loeys-Dietz syndrome;Loeys-Dietz syndrome 2, 610168 15731757;16928994;12975342 False 3 100;0;0 6.23 False ENSG00000163513 ENSG00000163513 HGNC:11773 TMCO1 gene TMCO1 Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal CRANIOFACIAL DYSMORPHISM, SKELETAL ANOMALIES, AND MENTAL RETARDATION SYNDROME;CFSMR;Cleft palate False 3 100;0;0 6.23 False ENSG00000143183 ENSG00000143183 HGNC:18188 TP63 gene TP63 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3, OMIM:604292;Hay-Wells syndrome, OMIM:106260;Limb-mammary syndrome, OMIM:603543;Orofacial cleft 8, OMIM:618149;Rapp-Hodgkin syndrome, OMIM:129400;Split-hand/foot malformation 4, OMIM:605289 False 3 100;0;0 6.23 False ENSG00000073282 ENSG00000073282 HGNC:15979 TRAPPC9 gene TRAPPC9 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 13, OMIM:613192 20004764;30853973 False 3 100;0;0 6.23 False ENSG00000167632 ENSG00000167632 HGNC:30832 TRIM37 gene TRIM37 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MULIBREY NANISM False 3 100;0;0 6.23 False ENSG00000108395 ENSG00000108395 HGNC:7523 TRRAP gene TRRAP Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Developmental delay with or without dysmorphic facies and autism, OMIM:618454 30827496;37010288 False 3 100;0;0 6.23 False ENSG00000196367 ENSG00000196367 HGNC:12347 TUBB gene TUBB Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown SKIN CREASES, CONGENITAL SYMMETRIC CIRCUMFERENTIAL, 1; CSCSC1 False 3 100;0;0 6.23 False ENSG00000196230 ENSG00000196230 HGNC:20778 TXNL4A gene TXNL4A Expert Review Green;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal BURN-MCKEOWN SYNDROME;BMKS;Cleft palate 25434003 False 3 100;0;0 6.23 False ENSG00000141759 ENSG00000141759 HGNC:30551 USP9X gene USP9X Expert Review Green;Literature Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Mental retardation, X-linked 99 300919 XLR;Mental retardation, X-linked 99, syndromic, female-restricted 300968 26833328 False 3 100;0;0 6.23 False ENSG00000124486 ENSG00000124486 HGNC:12632 WNT5A gene WNT5A Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ROBINOW SYNDROME, AUTOSOMAL DOMINANT 1; DRS1 False 3 100;0;0 6.23 False ENSG00000114251 ENSG00000114251 HGNC:12784 XYLT1 gene XYLT1 Expert Review Green Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Desbuquois dysplasia 2, OMIM:615777;Desbuquois dysplasia 2, MONDO:0014343 23982343;24581741;22711505;30554721 False 3 100;0;0 6.23 False ENSG00000103489 ENSG00000103489 HGNC:15516 ZC4H2 gene ZC4H2 Expert Review Green;Literature;NHS GMS Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Wieacker-Wolff syndrome, female-restricted, OMIM:301041 31206972;37010288 False 3 100;0;0 6.23 False ENSG00000126970 ENSG00000126970 HGNC:24931 ZEB2 gene ZEB2 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted MOWAT-WILSON SYNDROME; MOWS False 3 100;0;0 6.23 False ENSG00000169554 ENSG00000169554 HGNC:14881 ZIC2 gene ZIC2 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted HOLOPROSENCEPHALY 5; HPE5 19955556 False 3 100;0;0 6.23 False ENSG00000043355 ENSG00000043355 HGNC:12873 ZIC3 gene ZIC3 Expert Review Green Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females VACTERL ASSOCIATION, X-LINKED, WITH OR WITHOUT HYDROCEPHALUS; VACTERLX False 3 100;0;0 6.23 False ENSG00000156925 ENSG00000156925 HGNC:12874 ZSWIM6 gene ZSWIM6 Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown ACROMELIC FRONTONASAL DYSOSTOSIS; AFND 25105228 False 3 100;0;0 6.23 False ENSG00000130449 ENSG00000130449 HGNC:29316 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 ACBD5 gene ACBD5 Expert Review Red;Victorian Clinical Genetics Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Retinal dystrophy with leukodystrophy, OMIM:618863 23105016;27899449;27799409;33427402 False 1 0;0;100 6.23 False ENSG00000107897 ENSG00000107897 HGNC:23338 ADNP gene ADNP Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Helsmoortel-van der Aa syndrome, OMIM:615873 29724491;37010288 False 1 0;0;100 6.23 False ENSG00000101126 ENSG00000101126 HGNC:15766 ALG9 gene ALG9 Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal GILLESSEN-KAESBACH-NISHIMURA SYNDROME; GIKANIS False 1 0;0;100 6.23 False ENSG00000086848 ENSG00000086848 HGNC:15672 ARCN1 gene ARCN1 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay 617164 27476655 False 1 0;0;100 6.23 False ENSG00000095139 ENSG00000095139 HGNC:649 ATRX gene ATRX Expert Review Red Clefting Musculoskeletal MENTAL RETARDATION-HYPOTONIC FACIES SYNDROME, X-LINKED, 1; MRXHF1 9788563 False 1 0;0;100 6.23 False ENSG00000085224 ENSG00000085224 HGNC:886 B3GAT3 gene B3GAT3 Expert Review Red Clefting Musculoskeletal MULTIPLE JOINT DISLOCATIONS, SHORT STATURE, AND CRANIOFACIAL DYSMORPHISM WITH OR WITHOUT CONGENITAL HEART DEFECTS; JDSCD False 1 0;0;100 6.23 False ENSG00000149541 ENSG00000149541 HGNC:923 BMP4 gene BMP4 Expert Review Red;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;Victorian Clinical Genetics Services Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Orofacial cleft 11, 600625;Cleft Lip with or without Cleft Palate;Orofacial Cleft;Cleft lip with or without cleft palate, non syndromic, 11;MICROPHTHALMIA, SYNDROMIC 6;MCOPS6, OROFACIAL CLEFT 11;OFC11;Cleft lip False 1 0;50;50 6.23 False ENSG00000125378 ENSG00000125378 HGNC:1071 CANT1 gene CANT1 Expert Review Red Clefting Musculoskeletal DESBUQUOIS DYSPLASIA 1; DBQD1 27881841 False 1 0;0;100 6.23 False ENSG00000171302 ENSG00000171302 HGNC:19721 CASK gene CASK Expert Review Red Clefting Musculoskeletal MENTAL RETARDATION AND MICROCEPHALY WITH PONTINE AND CEREBELLAR HYPOPLASIA; MICPCH False 1 0;0;100 6.23 False ENSG00000147044 ENSG00000147044 HGNC:1497 CDK13 gene CDK13 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 29222009;37010288 False 1 0;0;100 6.23 False ENSG00000065883 ENSG00000065883 HGNC:1733 CDKL5 gene CDKL5 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 37010288 False 1 0;0;100 6.23 False ENSG00000008086 ENSG00000008086 HGNC:11411 CHD1 gene CHD1 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000153922 ENSG00000153922 HGNC:1915 CHD3 gene CHD3 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Snijders Blok-Campeau syndrome, OMIM:618205 37010288 False 1 0;0;100 6.23 False ENSG00000170004 ENSG00000170004 HGNC:1918 CHSY1 gene CHSY1 Expert list;Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Temtamy preaxial brachydactyly syndrome, 605282;TPBS 15365460 False 1 0;0;0 6.23 False ENSG00000131873 ENSG00000131873 HGNC:17198 CKAP2L gene CKAP2L Expert list;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Filippi syndrome, 272440 15365457;12416644 False 1 0;0;0 6.23 False ENSG00000169607 ENSG00000169607 HGNC:26877 COL9A3 gene COL9A3 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000092758 ENSG00000092758 HGNC:2219 CSNK2A1 gene CSNK2A1 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 37010288 False 1 0;0;100 6.23 False ENSG00000101266 ENSG00000101266 HGNC:2457 DIS3L2 gene DIS3L2 Expert list;Illumina TruGenome Clinical Sequencing Services Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Perlman syndrome, 267000 22306653;23486540;28328139 False 1 0;0;100 6.23 False ENSG00000144535 ENSG00000144535 HGNC:28648 DLG1 gene DLG1 Literature Clefting Musculoskeletal Unknown Non-syndromic cleft lip with or without cleft palate PMID: 28926086 False 1 0;0;100 6.23 False ENSG00000075711 ENSG00000075711 HGNC:2900 DNMT3B gene DNMT3B Expert list Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Immunodeficiency-centromeric instability-facial anomalies syndrome 1, 267000 17893117;23486536 False 1 0;0;100 6.23 False ENSG00000088305 ENSG00000088305 HGNC:2979 EDN1 gene EDN1 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000078401 ENSG00000078401 HGNC:3176 EP300 gene EP300 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Rubinstein-Taybi syndrome 2, OMIM:613684 27648933;37010288 False 1 0;0;100 6.23 False ENSG00000100393 ENSG00000100393 HGNC:3373 FAM111A gene FAM111A Expert list;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Gracile bone dysplasia; 602361 16086393;23684011 False 1 0;0;100 6.23 False ENSG00000166801 ENSG00000166801 HGNC:24725 FANCL gene FANCL Expert list;Expert Review Red;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Fanconi anemia, complementation group L, 614083 25754594 False 1 0;0;100 6.23 False ENSG00000115392 ENSG00000115392 HGNC:20748 FOXE1 gene FOXE1 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000178919 ENSG00000178919 HGNC:3806 FREM2 gene FREM2 Expert list;Expert Review Red;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Fraser syndrome, 219000 16894541;15838507;18203166;18671281 False 1 0;0;100 6.23 False ENSG00000150893 ENSG00000150893 HGNC:25396 GATA6 gene GATA6 Expert Review Red Clefting Musculoskeletal Unknown CONOTRUNCAL HEART MALFORMATIONS; CTHM 27391658 False 1 0;0;100 6.23 False ENSG00000141448 ENSG00000141448 HGNC:4174 GDF1 gene GDF1 Expert Review Red Clefting Musculoskeletal Unknown CONOTRUNCAL HEART MALFORMATIONS; CTHM 16564040 False 1 0;0;100 6.23 False ENSG00000130283 ENSG00000130283 HGNC:4214 GMNN gene GMNN Expert list;Expert Review Red;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Meier-Gorlin syndrome 6, OMIM:616835 26637980 False 1 0;0;0 6.23 False ENSG00000112312 ENSG00000112312 HGNC:17493 GNAI3 gene GNAI3 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000065135 ENSG00000065135 HGNC:4387 GRIP1 gene GRIP1 Expert list;Expert Review Red;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Fraser syndrome, 219000 16894541;18000968;22510445 False 1 0;0;100 6.23 False ENSG00000155974 ENSG00000155974 HGNC:18708 GYPE gene GYPE Clefting Musculoskeletal Unknown False 1 0;100;0 6.23 False ENSG00000197465 ENSG00000197465 HGNC:4705 HOXA2 gene HOXA2 Expert Review Red;Illumina TruGenome Clinical Sequencing Services;Victorian Clinical Genetics Services Clefting Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Microtia, Hearing Impairment, and Cleft Palate;Ear anomalies and orofacial clefting;?Microtia with or without hearing impairment (includes clefting), 612290, (MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown);?Microtia with or without hearing impairment (includes clefting), 612290, (BIALLELIC, autosomal or pseudoautosomal);Cleft palate 18394579;23775976;27503514 False 1 0;0;100 6.23 False ENSG00000105996 ENSG00000105996 HGNC:5103 INTS1 gene INTS1 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000164880 ENSG00000164880 HGNC:24555 KANSL1 gene KANSL1 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Koolen-De Vries syndrome, 610443; KDVS 22544363; 20301783 False 1 0;0;100 6.23 False ENSG00000120071 ENSG00000120071 HGNC:24565 KIF22 gene KIF22 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Spondyloepimetaphyseal dysplasia with joint laxity, type 2, 603546; SEMDJL2 22653704 False 1 0;0;100 6.23 False ENSG00000079616 ENSG00000079616 HGNC:6391 LMX1B gene LMX1B Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Nail-patella syndrome, 161200 2012138 False 1 0;0;100 6.23 False ENSG00000136944 ENSG00000136944 HGNC:6654 MAGEL2 gene MAGEL2 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Schaaf-Yang syndrome, OMIM:615547 31397880;37010288 False 1 0;0;100 6.23 False ENSG00000254585 ENSG00000254585 HGNC:6814 METTL23 gene METTL23 Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Mental retardation, autosomal recessive 44, 615942; MRT44 24501276 False 1 0;0;100 6.23 False ENSG00000181038 ENSG00000181038 HGNC:26988 MYCN gene MYCN Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cleft lip with or without cleft palate, MONDO:0016034 34590686 False 1 0;0;100 6.23 False ENSG00000134323 ENSG00000134323 HGNC:7559 NBN gene NBN Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Nijmegen breakage syndrome, 251260; NBS 22373003; 3857858 False 1 0;0;100 6.23 False ENSG00000104320 ENSG00000104320 HGNC:7652 NKX2-5 gene NKX2-5 Expert Review Red Clefting Musculoskeletal Unknown CONOTRUNCAL HEART MALFORMATIONS; CTHM 22155005 False 1 0;0;100 6.23 False ENSG00000183072 ENSG00000183072 HGNC:2488 NKX2-6 gene NKX2-6 Expert Review Red Clefting Musculoskeletal Unknown CONOTRUNCAL HEART MALFORMATIONS; CTHM False 1 0;0;100 6.23 False ENSG00000180053 ENSG00000180053 HGNC:32940 NSDHL gene NSDHL Expert Review Red Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females CONGENITAL HEMIDYSPLASIA WITH ICHTHYOSIFORM ERYTHRODERMA AND LIMB DEFECTS False 1 0;0;100 6.23 False ENSG00000147383 ENSG00000147383 HGNC:13398 PGAP2 gene PGAP2 Expert Review Red Clefting Musculoskeletal Unknown HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 3; HPMRS3 False 1 0;0;100 6.23 False ENSG00000148985 ENSG00000148985 HGNC:17893 PIGA gene PIGA Expert Review Red Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 2; MCAHS2 22305531;22514539 False 1 0;0;100 6.23 False ENSG00000165195 ENSG00000165195 HGNC:8957 PIGL gene PIGL Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal COLOBOMA, CONGENITAL HEART DISEASE, ICHTHYOSIFORM DERMATOSIS, MENTAL RETARDATION, AND EAR ANOMALIES SYNDROME; CHIME 28371479 False 1 0;0;100 6.23 False ENSG00000108474 ENSG00000108474 HGNC:8966 PIK3R2 gene PIK3R2 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1, OMIM:603387 False 1 0;0;100 6.23 False ENSG00000105647 ENSG00000105647 HGNC:8980 PLEKHA5 gene PLEKHA5 Expert list Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown cleft lip 29805042 False 1 0;0;100 6.23 False ENSG00000052126 ENSG00000052126 HGNC:30036 POLA1 gene POLA1 Literature Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females 31006512;37010288 False 1 0;0;100 6.23 False ENSG00000101868 ENSG00000101868 HGNC:9173 POLR2A gene POLR2A Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder with hypotonia and variable intellectual and behavioral abnormalities, OMIM:618603 31353023;37010288 False 1 0;0;100 6.23 False ENSG00000181222 ENSG00000181222 HGNC:9187 POMT1 gene POMT1 Expert list Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 1, 236670 12369018 False 1 0;0;0 6.23 False ENSG00000130714 ENSG00000130714 HGNC:9202 POMT2 gene POMT2 Expert list Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 2, 613150 15894594 False 1 0;0;0 6.23 False ENSG00000009830 ENSG00000009830 HGNC:19743 PQBP1 gene PQBP1 Expert list Clefting Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females Renpenning syndrome, 309500 7943045 False 1 0;0;0 6.23 False ENSG00000102103 ENSG00000102103 HGNC:9330 PSAT1 gene PSAT1 Expert list Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Neu-Laxova syndrome 2, 616038 25152457 False 1 0;0;0 6.23 False ENSG00000135069 ENSG00000135069 HGNC:19129 PTDSS1 gene PTDSS1 Expert list;Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Lenz-Majewski hyperostotic dwarfism, 151050;progressive sclerosis and hyperostosis of skull, vertebra and tubular bones;growth restriction;broad prominent forehead;delayed closure of the fontanelles;brachydactyly of fingers and toes;proximal symphalangism cutis laxa;dental enamel hypoplasia;choanal atresia 15194948;24241535;25363158;26117586 False 1 0;0;100 6.23 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000156471 ENSG00000156471 HGNC:9587 PUF60 gene PUF60 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Verheij syndrome, OMIM:615583 24140112;27804958;37010288 False 1 0;0;100 6.23 False ENSG00000179950 ENSG00000179950 HGNC:17042 RAI1 gene RAI1 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown SMITH-MAGENIS SYNDROME; SMS False 1 0;0;100 6.23 False ENSG00000108557 ENSG00000108557 HGNC:9834 RBM8A gene RBM8A Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal THROMBOCYTOPENIA-ABSENT RADIUS SYNDROME; TAR False 1 0;0;100 6.23 False ENSG00000131795 ENSG00000265241 HGNC:9905 RPL11 gene RPL11 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000142676 ENSG00000142676 HGNC:10301 RPS17 gene RPS17 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown DIAMOND-BLACKFAN ANEMIA 4; DBA4 False 1 0;0;100 6.23 False ENSG00000182774 ENSG00000182774 HGNC:10397 RPS19 gene RPS19 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown DIAMOND-BLACKFAN ANEMIA 1; DBA1 False 1 0;0;100 6.23 False ENSG00000105372 ENSG00000105372 HGNC:10402 RSPO2 gene RSPO2 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft lip False 1 0;0;0 6.23 False ENSG00000147655 ENSG00000147655 HGNC:28583 SELENOI gene SELENOI Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000138018 ENSG00000138018 HGNC:29361 SIN3A gene SIN3A Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Witteveen-Kolk syndrome, OMIM:613406 33437032;37010288 False 1 0;0;100 6.23 False ENSG00000169375 ENSG00000169375 HGNC:19353 SIX5 gene SIX5 Expert Review Red;NHS GMS Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Branchiootorenal syndrome 2, OMIM:610896 False 1 33;0;67 6.23 False ENSG00000177045 ENSG00000177045 HGNC:10891 SMAD2 gene SMAD2 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Loeys-Dietz syndrome 29967133;29392890 False 1 0;100;0 6.23 False ENSG00000175387 ENSG00000175387 HGNC:6768 SMOC1 gene SMOC1 Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MICROPHTHALMIA WITH LIMB ANOMALIES; MLA False 1 0;0;100 6.23 False ENSG00000198732 ENSG00000198732 HGNC:20318 SOX11 gene SOX11 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism, OMIM:615866 29437512;37010288 False 1 0;0;100 6.23 False ENSG00000176887 ENSG00000176887 HGNC:11191 SOX2 gene SOX2 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown MICROPHTHALMIA, SYNDROMIC 3; MCOPS3 False 1 0;0;100 6.23 False ENSG00000181449 ENSG00000181449 HGNC:11195 SOX5 gene SOX5 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 37010288 False 1 0;0;100 6.23 False ENSG00000134532 ENSG00000134532 HGNC:11201 STIL gene STIL Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MICROCEPHALY 7, PRIMARY, AUTOSOMAL RECESSIVE; MCPH7 False 1 0;0;100 6.23 False ENSG00000123473 ENSG00000123473 HGNC:10879 STRA6 gene STRA6 Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MICROPHTHALMIA, SYNDROMIC 9; MCOPS9 False 1 0;0;100 6.23 False ENSG00000137868 ENSG00000137868 HGNC:30650 STXBP1 gene STXBP1 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 4; EIEE4 False 1 0;0;100 6.23 False ENSG00000136854 ENSG00000136854 HGNC:11444 SUMO1 gene SUMO1 Expert Review Red;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Orofacial cleft 10, 613705;Cleft Lip with or without Cleft Palate 22492558 False 1 0;0;100 6.23 False ENSG00000116030 ENSG00000116030 HGNC:12502 TCF12 gene TCF12 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Craniosynostosis 3, OMIM:615314 23354436;31353793;37010288 False 1 0;0;100 6.23 False ENSG00000140262 ENSG00000140262 HGNC:11623 TFAP2B gene TFAP2B Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft lip False 1 0;0;0 6.23 False ENSG00000008196 ENSG00000008196 HGNC:11743 TGFB2 gene TGFB2 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Loeys-Dietz syndrome 4, 614816 29392890 False 1 0;100;0 6.23 False ENSG00000092969 ENSG00000092969 HGNC:11768 TSR2 gene TSR2 Victorian Clinical Genetics Services Clefting Musculoskeletal Cleft palate False 1 0;0;0 6.23 False ENSG00000158526 ENSG00000158526 HGNC:25455 TWIST2 gene TWIST2 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown BARBER-SAY SYNDROME; BBRSAY False 1 0;0;100 6.23 False ENSG00000233608 ENSG00000233608 HGNC:20670 UBB gene UBB Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Cleft palate, isolated, 119540 False 1 0;0;100 6.23 False ENSG00000170315 ENSG00000170315 HGNC:12463 UQCC2 gene UQCC2 Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Mitochondrial complex III deficiency, nuclear type 7, OMIM:615824 24385928 False 1 0;0;100 6.23 False ENSG00000137288 ENSG00000137288 HGNC:21237 VAX1 gene VAX1 Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal MICROPHTHALMIA, SYNDROMIC 11; MCOPS11 22095910 False 1 0;0;100 6.23 False ENSG00000148704 ENSG00000148704 HGNC:12660 WASHC5 gene WASHC5 Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal RITSCHER-SCHINZEL SYNDROME 1; RTSC1 24065355 False 1 0;0;100 6.23 False ENSG00000164961 ENSG00000164961 HGNC:28984 WDR26 gene WDR26 Literature Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 37010288 False 1 0;0;100 6.23 False ENSG00000162923 ENSG00000162923 HGNC:21208 WNT3 gene WNT3 Expert Review Red Clefting Musculoskeletal BIALLELIC, autosomal or pseudoautosomal TETRAAMELIA SYNDROME, AUTOSOMAL RECESSIVE; TETAMS 14872406 False 1 0;0;100 6.23 False ENSG00000108379 ENSG00000108379 HGNC:12782 YAP1 gene YAP1 Expert Review Red Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted COLOBOMA, OCULAR, WITH OR WITHOUT HEARING IMPAIRMENT, CLEFT LIP/PALATE, AND/OR MENTAL RETARDATION; COB1 24462371 False 1 0;0;100 6.23 False ENSG00000137693 ENSG00000137693 HGNC:16262 ISCA-37393-Gain region Expert Review Green;ClinGen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown PMID 22890013: variable phenotype including developmental delay, ocular coloboma, preauricular tags/pits, cleft palate, skeletal defects, heart defects, urogenital defect, anal defect, hearing loss, clinodactyly of fifth fingers, umbilical hernia, accessory spleen, strabismus, shortening of the fifth finger. PMID 22495764: Inter and intra individual variability of phenotype, mosaic. PMID 11693792: preauricular skin tags and pits, downslanting palpebral fissures, hypertelorism, ectopic anus, hypospadias, and hypoplastic left heart syndrome;115470 11693792;22890013;22495764 False 3 0;0;0 6.23 False 22 16912063 18109094 3 60 cnv_gain 22q11.21 recurrent (Cat eye syndrome) region (includes CECR2) Gain ISCA-37423-Gain region Expert Review Green;ClinGen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Behavioral problems, cleft lip and/or palate, macrocephaly, and seizures were confirmed as additional features among the new patients, and novel features included neonatal respiratory distress, attention deficit hyperactivity disorder (ADHD), ocular anomalies, balance problems, hypotonia, and hydrocele.;mild to moderate developmental delay, intellectual disability, mild facial dysmorphism (incl. prominent forehead, arched eyebrows, broad nasal bridge, upturned nares, cleft lip and/or palate) and congenital cardiac anomalies (e.g., atrioventricular septal defect). Other reported features include macrocephaly, behavioral abnormalities (e.g., attention deficit disorder), seizures, hypotonia and ocular and digital anomalies (poly/syndactyly);congenital heart disease;8p23.1 duplication syndrome 21933911;23345203 False 3 100;0;0 6.23 False 8 8242542 11908820 2 60 cnv_gain 8p23.1 recurrent region (includes GATA4) Gain ISCA-37446-Loss region Expert Review Green;ClinGen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown 188400;neonatal hypocalcemia, which may present as tetany or seizures, due to hypoplasia of the parathyroid glands, and susceptibility to infection due to a deficit of T cells;micrognathia;clefting;Hearing deficits;Velocardiofacial syndrome;cardiac malformations;DiGeorge syndrome False 3 0;0;0 6.23 False 22 18924718 21111383 3 60 cnv_loss 22q11.2 recurrent (DGS/VCFS) region (proximal, A-D) (includes TBX1) Loss ISCA-37467-Gain region Expert Review Green;ClinGen Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown human triphalangeal thumb and polysyndactyly (TPT-PS) phenotype;174500;Triphalangeal thumbpolysyndactyly syndrome;syndactyly type IV with tibial hypoplasia 19291772;18417549;18178630 False 3 0;0;0 6.23 False 7 156791102 156791874 3 60 cnv_gain 7q36.3 ZRS (SHH cis-regulatory) duplication region (within LMBR1 intron 5) Gain ISCA-46303-Loss region ClinGen;Expert Review Green Clefting Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown 24934569;26663529;19234473 False 3 100;0;0 6.23 False 17 69896855 71796293 3 60 cnv_loss SOX9 upstream enhancer region Loss