ADAMTS20

protein-coding

ADAM metallopeptidase with thrombospondin type 1 motif 20, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Gene summary

The protein encoded by this gene is a member of the ADAMTS family of zinc-dependent proteases. The encoded protein has a signal peptide that is cleaved to release the mature peptide, which is secreted and found in the extracellular matrix. This protein may be involved in tissue remodeling. [provided by RefSeq, Sep 2011]

MANE transcript

NM_025003.5

Inheritance

—

ClinVar variants

U:255B:41

Top phenotype

ADAMTS20-related condition

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr12:43,353,866-43,552,203

External References & Databases

Ensembl (ENSG00000173157)

Transcript & Mutation Effects

hg38 • Region Span ~198.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ADAMTS20 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 271

not providedTotal: 11

ADAMTS20-related conditionTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025003.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	7 clinvar	1 clinvar	9
missense			252 clinvar	32 clinvar	1 clinvar	285
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	255	39	2	296

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025003.5	RefSeq	NP_079279.3	39	MANE Select
ENST00000389420.8	Ensembl	ENSP00000374071.3	39	MANE Select
ENST00000549670.5	Ensembl	ENSP00000447427.1	11	Standard
ENST00000553158.5	Ensembl	ENSP00000448341.1	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
O-glycosylation of TSR domain-containing proteins
O-linked glycosylation

Biological Process

proteolysis
positive regulation of signal transduction
extracellular matrix organization
negative regulation of apoptotic process
positive regulation of melanocyte differentiation

Molecular Function

metalloendopeptidase activity
zinc ion binding

Cellular Component

extracellular space
collagen-containing extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389420
Coding exons: 39
Length: 198056
Individuals with no LoFs: 125219
Homozygous LoFs: 0
Heterozygous LoFs: 391
Defined: 125610
p: 0.00156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.686	1038	978	1.06	0.0000485	12478
Missense (PolyPhen)		392	397.32	0.98662		4993
Synonymous	0.250	326	332	0.983	0.0000166	3412
Loss of Function	3.04	77	112	0.690	0.00000620	1366

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0015	notable
Latino/Admixed American	0.0019	0.0017	notable
Ashkenazi Jewish	0.0034	0.0034	notable
East Asian	0.0025	0.0023	notable
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.0015	0.0013	notable
South Asian	0.0024	0.0023	notable
Other	0.0016	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in tissue-remodeling process occurring in both normal and pathological conditions. May have a protease- independent function in the transport from the endoplasmic reticulum to the Golgi apparatus of secretory cargos, mediated by the GON domain.;

Recessive Scores

pRec: 0.0930

Intolerance Scores

LoFtool: 0.850
RVIS EVS: -0.75
RVIS percentile EVS: 13.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0458

Gene Damage Prediction

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