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 CDX2 gene CDX2 Expert Review Green;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Multiple congenital anomalies 29177441;32058622;34671974 False 3 100;0;0 1.35 False ENSG00000165556 ENSG00000165556 HGNC:1806 CHD4 gene CHD4 Expert Review Green;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Syndromic INTELLECTUAL DISABILITY with or without congenital heart disease;Sifrim-Hitz-Weiss syndrome 617159 False 3 100;0;0 1.35 True Other - please provide details in the comments ENSG00000111642 ENSG00000111642 HGNC:1919 CHD7 gene CHD7 Expert Review Green;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted CHARGE syndrome False 3 100;0;0 1.35 True ENSG00000171316 ENSG00000171316 HGNC:20626 EFTUD2 gene EFTUD2 Eligibility statement prior genetic testing;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted microcephaly, facial asymmetry, inner ear anomalies False 3 100;0;0 1.35 True ENSG00000108883 ENSG00000108883 HGNC:30858 FANCB gene FANCB Expert Review Green;Illumina TruGenome Clinical Sequencing Services;UKGTN VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) VACTERL Association with Hydrocephalus False 3 100;0;0 1.35 True ENSG00000181544 ENSG00000181544 HGNC:3583 FGF10 gene FGF10 Emory Genetics Laboratory;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted False 3 100;0;0 1.35 True ENSG00000070193 ENSG00000070193 HGNC:3666 HAAO gene HAAO Expert Review Green;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Multiple congenital malformations; VACTERL-like phenotype 27604308;17334708;28792876 False 3 0;0;0 1.35 False ENSG00000162882 ENSG00000162882 HGNC:4796 HOXA13 gene HOXA13 Expert Review;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 140000 9020844 False 3 100;0;0 1.35 True ENSG00000106031 ENSG00000106031 HGNC:5102 KYNU gene KYNU Expert Review Green;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Hydroxykynureninuria (Disorders of histidine, tryptophan or lysine metabolism); ?Hydroxykynureninuria, 236800; multiple congenital malformations; VACTERL-like phenotype 27604308;17334708;28792876 False 3 0;0;0 1.35 False ENSG00000115919 ENSG00000115919 HGNC:6469 MYCN gene MYCN Emory Genetics Laboratory;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted False 3 100;0;0 1.35 True ENSG00000134323 ENSG00000134323 HGNC:7559 PLVAP gene PLVAP Expert Review Green;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal Diarrhoea 10, protein-losing enteropathy type, OMIM:618183 29875123;29661969;26207260;31215290 False 3 100;0;0 1.35 False ENSG00000130300 ENSG00000130300 HGNC:13635 PUF60 gene PUF60 Expert Review;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Verheij syndrome, 615583;VRJS;Chromosome 8q24.3 deletion syndrome;PUF60 syndrome 28327570;27804958;24140112 False 3 100;0;0 1.35 False ENSG00000179950 ENSG00000179950 HGNC:17042 SALL1 gene SALL1 Emory Genetics Laboratory;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted False 3 100;0;0 1.35 True ENSG00000103449 ENSG00000103449 HGNC:10524 SALL4 gene SALL4 Emory Genetics Laboratory;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted False 3 100;0;0 1.35 True ENSG00000101115 ENSG00000101115 HGNC:15924 TBX3 gene TBX3 Emory Genetics Laboratory;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted False 3 100;0;0 1.35 True ENSG00000135111 ENSG00000135111 HGNC:11602 TBX5 gene TBX5 Emory Genetics Laboratory;Expert Review Green VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted False 3 100;0;0 1.35 True ENSG00000089225 ENSG00000089225 HGNC:11604 TRAP1 gene TRAP1 Expert Review Green;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes BIALLELIC, autosomal or pseudoautosomal VACTERL; CAKUT PMID: 24152966 - recessive mutations reported in 2 families with CAKUT, and 3 families with VACTERL. False 3 100;0;0 1.35 True ENSG00000126602 ENSG00000126602 HGNC:16264 WBP11 gene WBP11 Expert Review Green;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Vertebral, cardiac, tracheoesophageal, renal, and limb defects, OMIM:619227 33276377 False 3 100;0;0 1.35 False ENSG00000084463 ENSG00000084463 HGNC:16461 ZIC3 gene ZIC3 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) VACTERL Association, X-linked;Heterotaxy, visceral, 1, X-linked 306955 PMID: 21465648 False 3 0;0;100 1.35 True ENSG00000156925 ENSG00000156925 HGNC:12874 KIAA1217 gene KIAA1217 Expert Review Amber;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes BOTH monoallelic and biallelic, autosomal or pseudoautosomal vertebral malformations 32369272 False 2 0;100;0 1.35 False ENSG00000120549 ENSG00000120549 HGNC:25428 MIR17HG gene MIR17HG Expert Review Amber;Literature VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Feingold syndrome;Feingold syndrome 2, 614326;FS2;Brachydactyly with short stature and microcephaly 21892160;19344873;25391829;26360630 False 2 50;50;0 1.35 True ENSG00000215417 ENSG00000215417 HGNC:23564 ARHGAP31 gene ARHGAP31 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes Skeletal dysplasias are a heterogeneous group of more than 450 disorders with complex mechanisms. False 1 0;0;100 1.35 False ENSG00000031081 ENSG00000031081 HGNC:29216 BMP2 gene BMP2 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000125845 ENSG00000125845 HGNC:1069 BMPR1B gene BMPR1B Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000138696 ENSG00000138696 HGNC:1077 CC2D2A gene CC2D2A Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000048342 ENSG00000048342 HGNC:29253 CDH3 gene CDH3 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000062038 ENSG00000062038 HGNC:1762 CEP290 gene CEP290 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000198707 ENSG00000198707 HGNC:29021 CHSY1 gene CHSY1 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000131873 ENSG00000131873 HGNC:17198 ESCO2 gene ESCO2 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000171320 ENSG00000171320 HGNC:27230 FBLN1 gene FBLN1 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000077942 ENSG00000077942 HGNC:3600 FBXW4 gene FBXW4 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000107829 ENSG00000107829 HGNC:10847 FGFR2 gene FGFR2 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000066468 ENSG00000066468 HGNC:3689 FGFR3 gene FGFR3 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000068078 ENSG00000068078 HGNC:3690 FMN1 gene FMN1 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000248905 ENSG00000248905 HGNC:3768 GDF5 gene GDF5 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000125965 ENSG00000125965 HGNC:4220 GLI3 gene GLI3 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000106571 ENSG00000106571 HGNC:4319 GNAS gene GNAS Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000087460 ENSG00000087460 HGNC:4392 GREM1 gene GREM1 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000166923 ENSG00000166923 HGNC:2001 HDAC4 gene HDAC4 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000068024 ENSG00000068024 HGNC:14063 HOXD13 gene HOXD13 Emory Genetics Laboratory;Expert Review Red;Radboud University Medical Center, Nijmegen VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes Synpolydactyly, type II, 186000 False 1 0;0;100 1.35 True ENSG00000128714 ENSG00000128714 HGNC:5136 IHH gene IHH Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000163501 ENSG00000163501 HGNC:5956 KIF7 gene KIF7 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000166813 ENSG00000166813 HGNC:30497 LMBR1 gene LMBR1 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000105983 ENSG00000105983 HGNC:13243 LRP4 gene LRP4 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000134569 ENSG00000134569 HGNC:6696 MGP gene MGP Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000111341 ENSG00000111341 HGNC:7060 MKS1 gene MKS1 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000011143 ENSG00000011143 HGNC:7121 NIPBL gene NIPBL Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000164190 ENSG00000164190 HGNC:28862 NOG gene NOG Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000183691 ENSG00000183691 HGNC:7866 PIGV gene PIGV Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000060642 ENSG00000060642 HGNC:26031 PITX1 gene PITX1 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000069011 ENSG00000069011 HGNC:9004 PTEN gene PTEN Radboud University Medical Center, Nijmegen VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes Cowden syndrome 1, 158350Lhermitte-Duclos syndrome, 158350Bannayan-Riley-Ruvalcaba syndrome, 153480{Meningioma}, 607174{Glioma susceptibility 2}, 613028Macrocephaly/autism syndrome, 605309PTEN hamartoma tumor syndromeVATER association with macrocephaly and ventriculomegaly, 276950{Prostate cancer, somatic}, 176807Thyroid carcinoma, follicular, somatic, 188470Malignant melanoma, somatic, 155600Endometrial carcinoma, somatic, 608089Squamous cell carcinoma, head and neck, somatic, 275355 False 1 0;0;100 1.35 False ENSG00000171862 ENSG00000171862 HGNC:9588 PTHLH gene PTHLH Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000087494 ENSG00000087494 HGNC:9607 RECQL4 gene RECQL4 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000160957 ENSG00000160957 HGNC:9949 ROR2 gene ROR2 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000169071 ENSG00000169071 HGNC:10257 RPGRIP1L gene RPGRIP1L Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000103494 ENSG00000103494 HGNC:29168 SHH gene SHH Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000164690 ENSG00000164690 HGNC:10848 SOX9 gene SOX9 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000125398 ENSG00000125398 HGNC:11204 TBX15 gene TBX15 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000092607 ENSG00000092607 HGNC:11594 THPO gene THPO Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000090534 ENSG00000090534 HGNC:11795 TP63 gene TP63 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000073282 ENSG00000073282 HGNC:15979 WNT3 gene WNT3 Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000108379 ENSG00000108379 HGNC:12782 WNT7A gene WNT7A Emory Genetics Laboratory VACTERL-like phenotypes Limb disorders Dysmorphic and congenital abnormality syndromes False 1 0;0;100 1.35 False ENSG00000154764 ENSG00000154764 HGNC:12786