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													
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