ADAMTS1

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

Basic information

Region (hg38): 21:26835754-26845409

Links

ENSG00000154734 ∙ NCBI:9510 ∙ OMIM:605174 ∙ HGNC:217 ∙ Uniprot:Q9UHI8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant prognathism (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS1 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	6	10
missense		1	51	8	3	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					1	1
Total	0	1	51	12	10

Variants in ADAMTS1

This is a list of pathogenic ClinVar variants found in the ADAMTS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-26837599-T-G		not specified	Uncertain significance (May 23, 2023)
21-26837652-G-A		not specified	Uncertain significance (May 11, 2022)
21-26837652-G-C		not specified	Uncertain significance (Mar 20, 2023)
21-26837670-T-C			Likely benign (Sep 25, 2018)
21-26837760-G-A		not specified	Uncertain significance (Dec 09, 2023)
21-26837769-G-A		not specified	Uncertain significance (Aug 02, 2023)
21-26837892-C-T		not specified	Uncertain significance (Jan 06, 2023)
21-26837959-C-T		not specified	Uncertain significance (Jan 04, 2024)
21-26837985-C-T		not specified	Uncertain significance (Jan 23, 2024)
21-26838017-G-C			Benign (Sep 11, 2018)
21-26838024-G-C		not specified	Uncertain significance (May 11, 2022)
21-26838048-C-T		not specified	Uncertain significance (Jun 16, 2024)
21-26838049-G-A			Benign (Dec 31, 2019)
21-26838066-G-A		not specified	Uncertain significance (Aug 21, 2023)
21-26838096-C-A		not specified	Uncertain significance (Jul 06, 2022)
21-26838138-T-C			Likely benign (Dec 31, 2019)
21-26838155-T-C			Benign (Dec 31, 2019)
21-26838171-T-C		not specified	Uncertain significance (Jun 12, 2023)
21-26838216-C-T			Likely benign (Dec 31, 2019)
21-26838217-G-A		not specified	Uncertain significance (Nov 10, 2022)
21-26838229-C-T		not specified	Uncertain significance (Sep 14, 2022)
21-26838446-T-G		not specified	Uncertain significance (Jun 22, 2023)
21-26838448-G-A		not specified	Uncertain significance (Jul 14, 2023)
21-26839661-C-T			Likely benign (Mar 01, 2022)
21-26839678-A-G		not specified	Likely benign (May 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS1	protein_coding	protein_coding	ENST00000284984	9	9663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.716	0.284	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.667	504	548	0.920	0.0000283	6267
Missense in Polyphen		212	257.71	0.82264		3002
Synonymous	-0.0517	232	231	1.00	0.0000133	1895
Loss of Function	4.63	8	39.3	0.204	0.00000201	453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000117	0.000105
Middle Eastern	0.000164	0.000163
South Asian	0.000267	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves aggrecan, a cartilage proteoglycan, at the '1938-Glu-|-Leu-1939' site (within the chondroitin sulfate attachment domain), and may be involved in its turnover (By similarity). Has angiogenic inhibitor activity. Active metalloprotease, which may be associated with various inflammatory processes as well as development of cancer cachexia. May play a critical role in follicular rupture. {ECO:0000250, ECO:0000269|PubMed:10438512}.
• Pathway: VEGFA-VEGFR2 Signaling Pathway;Endochondral Ossification;Post-translational protein modification;Metabolism of proteins;Extracellular matrix organization;Degradation of the extracellular matrix;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.398
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.17

Haploinsufficiency Scores

• pHI: 0.475
• hipred: Y
• hipred_score: 0.793
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.829

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamts1
• Phenotype: endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype

Gene ontology

• Biological process: ovulation from ovarian follicle;kidney development;proteolysis;integrin-mediated signaling pathway;negative regulation of cell population proliferation;heart trabecula formation;positive regulation of G1/S transition of mitotic cell cycle;positive regulation of vascular smooth muscle cell proliferation;positive regulation of vascular associated smooth muscle cell migration
• Cellular component: basement membrane;cytoplasmic vesicle;collagen-containing extracellular matrix
• Molecular function: metalloendopeptidase activity;heparin binding;metallopeptidase activity;zinc ion binding