ADAMTS15

ADAM metallopeptidase with thrombospondin type 1 motif 15, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Basic information

Region (hg38): 11:130448645-130476645

Links

ENSG00000166106 ∙ NCBI:170689 ∙ OMIM:607509 ∙ HGNC:16305 ∙ Uniprot:Q8TE58 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Arthrogryposis, distal, type 12	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental; Musculoskeletal	35962790

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS15 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					4	4
missense			60	3	1	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	3	5

Variants in ADAMTS15

This is a list of pathogenic ClinVar variants found in the ADAMTS15 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-130449096-C-G		Arthrogryposis, distal, type 12	Pathogenic (Oct 19, 2023)
11-130449109-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-130449116-C-A		not specified	Uncertain significance (Oct 06, 2022)
11-130449151-T-C		not specified	Uncertain significance (May 25, 2022)
11-130449173-A-G		not specified	Uncertain significance (Sep 14, 2021)
11-130449217-G-C		not specified	Uncertain significance (Dec 13, 2021)
11-130449223-C-G		not specified	Uncertain significance (Jun 29, 2023)
11-130449224-T-A		not specified	Uncertain significance (Aug 15, 2023)
11-130449307-G-C		not specified	Uncertain significance (Jan 23, 2023)
11-130449520-G-A		not specified	Uncertain significance (Aug 29, 2023)
11-130449544-T-A		not specified	Uncertain significance (Aug 17, 2022)
11-130449620-T-A		not specified	Uncertain significance (May 08, 2023)
11-130449623-C-G		not specified	Uncertain significance (Aug 20, 2023)
11-130449626-G-A		not specified	Uncertain significance (Dec 08, 2023)
11-130449676-G-A			Benign (Dec 04, 2017)
11-130449742-A-G		not specified	Uncertain significance (Jan 26, 2022)
11-130449748-C-T		not specified	Uncertain significance (Apr 25, 2023)
11-130449895-G-A		not specified	Uncertain significance (Oct 27, 2022)
11-130461489-G-A		not specified	Uncertain significance (Sep 14, 2022)
11-130462101-A-G		not specified	Uncertain significance (Feb 16, 2023)
11-130462116-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-130462171-C-T		not specified	Uncertain significance (Nov 17, 2023)
11-130462176-C-G		not specified	Uncertain significance (Mar 01, 2023)
11-130462188-G-T		not specified	Uncertain significance (May 23, 2023)
11-130462209-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS15	protein_coding	protein_coding	ENST00000299164	8	27664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000167	0.999	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.508	553	588	0.941	0.0000354	6054
Missense in Polyphen		240	269.78	0.88961		2799
Synonymous	-0.682	280	266	1.05	0.0000170	2033
Loss of Function	2.80	15	32.1	0.467	0.00000151	367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000267
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000191	0.000185
Middle Eastern	0.000164	0.000163
South Asian	0.0000985	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.318
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.75

Haploinsufficiency Scores

• pHI: 0.346
• hipred: Y
• hipred_score: 0.725
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Adamts15

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular space;cell surface;collagen-containing extracellular matrix
• Molecular function: metalloendopeptidase activity;heparin binding;zinc ion binding;extracellular matrix binding