ADAMTS6

ADAM metallopeptidase with thrombospondin type 1 motif 6, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Basic information

Region (hg38): 5:65148738-65481920

Links

ENSG00000049192 ∙ NCBI:11174 ∙ OMIM:605008 ∙ HGNC:222 ∙ Uniprot:Q9UKP5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS6 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						0
missense		1	39	4	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	1	39	4	1

Variants in ADAMTS6

This is a list of pathogenic ClinVar variants found in the ADAMTS6 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-65170632-T-C		not specified	Uncertain significance (Oct 10, 2023)
5-65170679-C-T		not specified	Uncertain significance (Dec 01, 2022)
5-65170713-C-G		not specified	Uncertain significance (Jul 11, 2023)
5-65170715-G-A		not specified	Uncertain significance (Oct 25, 2024)
5-65172848-G-A		ADAMTS6-related disorder	Likely benign (Feb 15, 2023)
5-65172887-C-T		not specified	Uncertain significance (Jul 14, 2021)
5-65172888-G-A		not specified	Uncertain significance (Mar 06, 2023)
5-65172894-G-C		not specified	Uncertain significance (Nov 28, 2024)
5-65172942-T-C		not specified	Uncertain significance (May 31, 2023)
5-65172958-C-G		not specified	Uncertain significance (Feb 21, 2024)
5-65188086-C-T		Premature ovarian failure	Likely pathogenic (Mar 02, 2020)
5-65188135-C-T		not specified	Uncertain significance (Nov 29, 2024)
5-65188165-T-C		not specified	Uncertain significance (Mar 19, 2024)
5-65188199-C-G		not specified	Uncertain significance (Oct 26, 2022)
5-65197100-A-G		not specified	Uncertain significance (Aug 10, 2024)
5-65214898-T-C		not specified	Uncertain significance (Nov 09, 2024)
5-65214910-A-G		not specified	Uncertain significance (Apr 20, 2024)
5-65215458-T-C		not specified	Uncertain significance (Aug 09, 2021)
5-65215464-A-T		not specified	Uncertain significance (Jun 26, 2024)
5-65224338-T-C			Benign (Apr 04, 2018)
5-65224932-G-C		not specified	Uncertain significance (Nov 14, 2024)
5-65225010-C-T		not specified	Uncertain significance (Sep 13, 2023)
5-65225024-C-A		not specified	Uncertain significance (Apr 16, 2024)
5-65226121-C-G		not specified	Uncertain significance (Sep 24, 2024)
5-65226121-C-T		not specified	Uncertain significance (Oct 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS6	protein_coding	protein_coding	ENST00000381055	24	333185

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000217	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.09	402	618	0.650	0.0000322	7386
Missense in Polyphen		86	219.76	0.39134		2546
Synonymous	0.0637	205	206	0.994	0.0000102	2028
Loss of Function	6.59	8	65.5	0.122	0.00000343	764

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000630	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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: 0.120

Intolerance Scores

• loftool: 0.309
• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.9

Haploinsufficiency Scores

• pHI: 0.431
• hipred: Y
• hipred_score: 0.682
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamts6
• Phenotype: skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: cardiac septum development;proteolysis;aorta development;coronary vasculature development
• Cellular component: extracellular region
• Molecular function: metalloendopeptidase activity;metallopeptidase activity;metal ion binding