GeneBe

ADAMTS10

ADAM metallopeptidase with thrombospondin type 1 motif 10, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Basic information

Region (hg38): 19:8580240-8610735

Links

ENSG00000142303 ∙ NCBI:81794 ∙ OMIM:608990 ∙ HGNC:13201 ∙ Uniprot:Q9H324 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Weill-Marchesani syndrome 1 (Moderate), mode of inheritance: AR
  • Weill-Marchesani syndrome (Supportive), mode of inheritance: AD
  • Weill-Marchesani syndrome 1 (Definitive), mode of inheritance: AR
  • Weill-Marchesani syndrome 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Weill-Marchesani syndrome 1ARCardiovascular; OphthalmologicIndividuals can have cardiac anomalies, including long QTc, and awareness may allow for preventive/medical management, which may decrease morbidity and mortality; As the condition can include glaucoma, surveillance can allow early interventions that may potentially be beneficial related to preservation of visual statusCardiovascular; Musculoskeletal; Neurologic; Ophthalmologic11941487; 14598350; 15368195; 17663475

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS10 gene.

  • not_provided (806 variants)
  • Inborn_genetic_diseases (129 variants)
  • Weill-Marchesani_syndrome (84 variants)
  • Weill-Marchesani_syndrome_1 (47 variants)
  • ADAMTS10-related_disorder (22 variants)
  • not_specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030957.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
278
clinvar
5
clinvar
 288
missense
2
clinvar
8
clinvar
321
clinvar
15
clinvar
3
clinvar
 349
nonsense
9
clinvar
1
clinvar
1
clinvar
 11
start loss
0
frameshift
8
clinvar
1
clinvar
1
clinvar
 10
splice donor/acceptor (+/-2bp)
1
clinvar
3
clinvar
 4
Total 20 13 328 293 8

Highest pathogenic variant AF is 0.0000065799863

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ADAMTS10protein_codingprotein_codingENST00000270328 2430495
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.8430.1571257300181257480.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.634467200.6200.00005077077
Missense in Polyphen109255.080.427322605
Synonymous0.7822943120.9440.00002382241
Loss of Function5.671259.00.2040.00000313618

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003420.000333
Ashkenazi Jewish0.00009930.0000992
East Asian0.0001630.000163
Finnish0.00004790.0000462
European (Non-Finnish)0.00005320.0000527
Middle Eastern0.0001630.000163
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Metalloprotease that participate in microfibrils assembly. Microfibrils are extracellular matrix components occurring independently or along with elastin in the formation of elastic tissues. {ECO:0000269|PubMed:21402694}.;
Disease
DISEASE: Weill-Marchesani syndrome 1 (WMS1) [MIM:277600]: A rare connective tissue disorder characterized by short stature, brachydactyly, joint stiffness, and eye abnormalities including microspherophakia, ectopia lentis, severe myopia and glaucoma. {ECO:0000269|PubMed:15368195, ECO:0000269|PubMed:18567016}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

pRec
0.121

Intolerance Scores

loftool
0.476
rvis_EVS
-1.32
rvis_percentile_EVS
4.78

Haploinsufficiency Scores

pHI
0.288
hipred
Y
hipred_score
0.693
ghis
0.618

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.221

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Adamts10
Phenotype

Gene ontology

Biological process
proteolysis;biological_process
Cellular component
microfibril;collagen-containing extracellular matrix
Molecular function
molecular_function;metalloendopeptidase activity;protein binding;metal ion binding