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 ABL1 gene ABL1 Expert Review Amber;Literature;NHS GMS Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Congenital heart defects and skeletal malformations syndrome, 617602 28288113 False 2 50;50;0 8.46 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000097007 ENSG00000097007 HGNC:76 B9D1 gene B9D1 Emory Genetics Laboratory;Expert list;Expert Review Amber;Illumina TruGenome Clinical Sequencing Services;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Meckel syndrome 9, OMIM:614209;Meckel syndrome 9, MONDO:0013630;Joubert syndrome 27, OMIM:617120;Joubert syndrome 27, MONDO:0014927 21493627;24886560 False 2 33;33;33 8.46 False ENSG00000108641 ENSG00000108641 HGNC:24123 BTRC gene BTRC Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Split-hand/foot malformation 3, gene duplication syndrome, OMIM:246560;split hand-foot malformation 3, MONDO:0009525 19584065;18067070;12913067;16681918;27600068;30622331;35908152;36928426;18392654 False 2 0;100;0 8.46 False Other ENSG00000166167 ENSG00000166167 HGNC:1144 C16orf62 gene C16orf62 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal 3C/Ritscher-Schinzel-like syndrome 31712251 False 2 0;100;0 8.46 False ENSG00000103544 ENSG00000103544 HGNC:24641 CSNK1G1 gene CSNK1G1 Expert Review Amber;NHS GMS Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown early-onset epileptic encephalopathy and microcephaly 24463883;33009664 False 2 0;100;0 8.46 False ENSG00000169118 ENSG00000169118 HGNC:2454 DROSHA gene DROSHA Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Global developmental delay;Intellectual disability;Seizures;Cerebral white matter atrophy;Abnormality of the corpus callosum;Abnormality of movement;Stereotypic behavior;Abnormality of head or neck;Short foot 35405010 False 2 33;67;0 8.46 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000113360 ENSG00000113360 HGNC:17904 EN1 gene EN1 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal ENDOVE syndrome, limb-only type, MIM# 619217;ENDOVE syndrome, limb-brain type, MIM# 619218 33568816 False 2 100;0;0 8.46 False ENSG00000163064 ENSG00000163064 HGNC:3342 FBLN1 gene FBLN1 Emory Genetics Laboratory;Expert list;Expert Review Amber;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Skeletal dysplasia Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Synpolydactyly, 3/3'4, associated with metacarpal and metatarsal synostoses 608180 24084572 False 2 33;67;0 8.46 False ENSG00000077942 ENSG00000077942 HGNC:3600 FBXW4 gene FBXW4 Emory Genetics Laboratory;Expert list;Expert Review Amber;Illumina TruGenome Clinical Sequencing Services;UKGTN Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Split-hand/foot malformation 3, gene duplication syndrome, OMIM:246560;split hand-foot malformation 3, MONDO:0009525 19584065;18067070;12913067;16681918;27600068;30622331;35908152;36928426;18392654 False 2 100;0;0 8.46 False Other - please provide details in the comments ENSG00000107829 ENSG00000107829 HGNC:10847 GNPNAT1 gene GNPNAT1 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Rhizomelic skeletal dysplasia 32591345 False 2 0;100;0 8.46 False ENSG00000100522 ENSG00000100522 HGNC:19980 H2AFY gene H2AFY Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Liebenberg syndrome;brachydactyly-elbow wrist dysplasia syndrome, MONDO:0008520 23022097;23587911;30711920 False 2 50;50;0 8.46 False ENSG00000113648 ENSG00000113648 HGNC:4740 HDAC4 gene HDAC4 Emory Genetics Laboratory;Expert list;Expert Review Amber;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Albright hereditary osteodystrophy type 3;Brachydactyly-intellectual disability;Albright hereditary osteodystrophy type 3, Albright hereditary osteodystrophy-like syndrome, Brachydactyly-intellectual disability, Del(2)(q37) 600430;Albright hereditary osteodystrophy-like syndrome;Del(2)(q37) 600430 19365831;15521982;20691407;25402011 False 2 33;67;0 8.46 False ENSG00000068024 ENSG00000068024 HGNC:14063 HEATR3 gene HEATR3 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Anemia;Thrombocytopenia;Growth delay;Short stature;Abnormality of the skeletal system;Abnormality of finger;Abnormality of the thumb;Intellectual disability;Obesity;Abnormality of the face 35213692 False 2 0;100;0 8.46 False ENSG00000155393 ENSG00000155393 HGNC:26087 HNRNPK gene HNRNPK Expert Review Amber;NHS GMS;Other Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Orphanet:453499; OMIM:616580;Au-Kline syndrome:616580;Neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome due to a point mutation;Orphanet:453499 26173930;26638989;26954065 False 2 0;100;0 8.46 False ENSG00000165119 ENSG00000165119 HGNC:5044 IDH1 gene IDH1 Expert Review Amber;NHS GMS Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria OMIM:614875;metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria, MONDO:0013941;Maffucci syndrome, OMIM:614569;Maffucci syndrome, MONDO:0013808;Ollier disease/ Dyschondroplasia, OMIM:166000;Ollier disease, MONDO:0008145 24049096;22025298;22057234;22057236 False 2 33;67;0 8.46 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000138413 ENSG00000138413 HGNC:5382 LRRC8C gene LRRC8C Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted TIMES syndrome, OMIM:621056 39623139 False 2 0;100;0 8.46 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000171488 ENSG00000171488 HGNC:25075 MANBA gene MANBA Expert Review Amber;NHS GMS Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Beta-mannosidosis, 248510 2079835;16401745;18980795 False 2 50;50;0 8.46 False ENSG00000109323 ENSG00000109323 HGNC:6831 MBTPS2 gene MBTPS2 Expert list;Expert Review Amber Skeletal dysplasia Musculoskeletal X-LINKED: hemizygous mutation in males, biallelic mutations in females Osteogenesis imperfecta, type XIX, OMIM:301014;osteogenesis imperfecta, type 19, MONDO:0049223 27380894 False 2 33;67;0 8.46 False ENSG00000012174 ENSG00000012174 HGNC:15455 MIA3 gene MIA3 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal ?Odontochondrodysplasia 2 with hearing loss and diabetes, OMIM:619269 32101163;33778321;40948380;40119123;40130161;21606205;34680893 False 2 33;0;67 8.46 False ENSG00000154305 ENSG00000154305 HGNC:24008 MIR17HG gene MIR17HG Expert list;Expert Review Amber;NHS GMS;Radboud University Medical Center, Nijmegen Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted FS2;Brachydactyly with short stature and microcephaly;Microcephaly-oculo-digito-esophageal-duodenal syndrome;Feingold syndrome 2, 614326 25391829;21892160;26360630;19344873 False 2 25;50;25 8.46 False ENSG00000215417 ENSG00000215417 HGNC:23564 MMP9 gene MMP9 Emory Genetics Laboratory;Expert list;Expert Review Amber;Illumina TruGenome Clinical Sequencing Services;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Metaphyseal anadysplasia 2 613073 28342220;19615667 False 2 67;33;0 8.46 False ENSG00000100985 ENSG00000100985 HGNC:7176 NMNAT1 gene NMNAT1 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Spondyloepiphyseal dysplasia, sensorineural hearing loss, intellectual disability, and Leber congenital amaurosis (SHILCA), MIM#619260 32533184;33668384 False 2 50;50;0 8.46 False ENSG00000173614 ENSG00000173614 HGNC:17877 NRCAM gene NRCAM Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with neuromuscular and skeletal abnormalities, OMIM:619833 35108495 False 2 100;0;0 8.46 False ENSG00000091129 ENSG00000091129 HGNC:7994 PAM16 gene PAM16 Expert list;Expert Review Amber;NHS GMS Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Spondylometaphyseal dysplasia, Megarbane-Dagher-Melike type 613320 24786642;27354339 False 2 67;33;0 8.46 False ENSG00000217930 ENSG00000217930 HGNC:29679 PDIA6 gene PDIA6 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Asphyxiating thoracic dystrophy (ATD) syndrome and infantile onset diabetes;Polycystic kidney dysplasia, HP:0000113;Diabetes mellitus, HP:0000819;Microcephaly, HP:0000252 33495992;34487921;35856135;40974269 False 2 0;100;0 8.46 False ENSG00000143870 ENSG00000143870 HGNC:30168 PFN1 gene PFN1 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Paget s disease of bone;bone Paget disease MONDO:0005382 32392277;31991009;31346562;32589291;22801503 False 2 0;100;0 8.46 False ENSG00000108518 ENSG00000108518 HGNC:8881 PLEKHM1 gene PLEKHM1 Expert list;Expert Review Amber;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Skeletal dysplasia Musculoskeletal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Osteopetrosis, autosomal recessive 6 - 611497;Osteopetrosis, autosomal recessive 6 611497;Osteopetrosis, autosomal dominant 3 - 618107 17404618;27291868;17997709;21054159;28290981;32415263 False 2 50;50;0 8.46 False ENSG00000225190 ENSG00000225190 HGNC:29017 RAD21 gene RAD21 Emory Genetics Laboratory;Expert list;Expert Review Amber;NHS GMS;Radboud University Medical Center, Nijmegen Skeletal dysplasia Musculoskeletal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cornelia de Lange syndrome 4, OMIM:614701 22633399;30716475;24378232;27882533;27620904;31334757;32193685 False 2 67;33;0 8.46 False ENSG00000164754 ENSG00000164754 HGNC:9811 SCNM1 gene SCNM1 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Orofaciodigital syndrome XIX, OMIM:620107;orofaciodigital syndrome 19, MONDO:0859310 36084634;41291844 False 2 100;0;0 8.46 False ENSG00000163156 ENSG00000163156 HGNC:23136 SIK3 gene SIK3 Expert Review Amber;NHS GMS Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal ?Spondyloepimetaphyseal dysplasia, Krakow type, OMIM:618162;spondyloepimetaphyseal dysplasia, Krakow type, MONDO:0032571 30232230;22318228 False 2 33;67;0 8.46 False ENSG00000160584 ENSG00000160584 HGNC:29165 SLC35B2 gene SLC35B2 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Abnormality of the skeletal system;Short long bone;Short stature;Abnormality of epiphysis morphology;Scoliosis;Multiple joint dislocation;Global develpmental delay;Intellectual disability;CNS hypomyelination;Abnormality of the corpus callosum;Cerebral atrophy;Abnormality of the amniotic fluid 35325049 False 2 0;100;0 8.46 False ENSG00000157593 ENSG00000157593 HGNC:16872 SUCO gene SUCO Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Osteogenesis imperfecta, MONDO:0019019;skeletal dysplasia, HP:0002652;osteopenia 29620724;20440000 False 2 0;100;0 8.46 False ENSG00000094975 ENSG00000094975 HGNC:1240 TMEM251 gene TMEM251 Expert Review Amber;Literature Skeletal dysplasia Musculoskeletal BIALLELIC, autosomal or pseudoautosomal Dysostosis multiplex, Ain-Naz type, OMIM:19345;severe short stature 33252156 False 2 0;100;0 8.46 False ENSG00000153485 ENSG00000153485 HGNC:20218