ADAMTS20

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

Basic information

Region (hg38): 12:43353865-43552203

Links

ENSG00000173157 ∙ NCBI:80070 ∙ OMIM:611681 ∙ HGNC:17178 ∙ Uniprot:P59510 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS20 gene.

• Inborn genetic diseases (77 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS20 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	1	5
missense			72	6	1	79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	72	10	2

Variants in ADAMTS20

This is a list of pathogenic ClinVar variants found in the ADAMTS20 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-43356546-A-C		not specified	Uncertain significance (Dec 04, 2023)
12-43369344-A-C		not specified	Likely benign (Mar 29, 2022)
12-43375382-T-C		not specified	Uncertain significance (Oct 03, 2022)
12-43375448-C-G		not specified	Uncertain significance (Jul 20, 2022)
12-43376063-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-43376118-G-C		not specified	Uncertain significance (Jan 18, 2022)
12-43376330-C-T		not specified	Uncertain significance (Oct 24, 2023)
12-43376551-C-A		not specified	Uncertain significance (Jun 13, 2022)
12-43376601-G-T		not specified	Uncertain significance (Nov 17, 2023)
12-43376619-C-G		not specified	Uncertain significance (Nov 09, 2021)
12-43376634-A-G		not specified	Uncertain significance (Aug 10, 2021)
12-43377445-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-43377512-G-A			Likely benign (Oct 01, 2022)
12-43377523-T-C		not specified	Uncertain significance (Jan 10, 2022)
12-43383583-A-G		not specified	Uncertain significance (Aug 22, 2023)
12-43383590-T-G		not specified	Uncertain significance (Jul 16, 2021)
12-43383623-G-C		not specified	Uncertain significance (Mar 02, 2023)
12-43383691-C-T		not specified	Likely benign (Mar 05, 2024)
12-43383839-C-T		not specified	Uncertain significance (Jul 15, 2021)
12-43383877-C-T		not specified	Uncertain significance (Jun 30, 2023)
12-43383959-A-G		not specified	Uncertain significance (Apr 08, 2022)
12-43399158-C-A			Uncertain significance (Jul 03, 2020)
12-43399184-A-G		not specified	Uncertain significance (Feb 13, 2024)
12-43425515-G-A		not specified	Uncertain significance (Sep 01, 2021)
12-43425576-T-C		not specified	Likely benign (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS20	protein_coding	protein_coding	ENST00000389420	39	198056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.45e-38	0.816	125219	0	391	125610	0.00156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.686	1038	978	1.06	0.0000485	12478
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00345	0.00342
Ashkenazi Jewish	0.00338	0.00338
East Asian	0.00245	0.00234
Finnish	0.000324	0.000324
European (Non-Finnish)	0.00152	0.00128
Middle Eastern	0.00245	0.00234
South Asian	0.00244	0.00226
Other	0.00158	0.00147

dbNSFP

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

Recessive Scores

• pRec: 0.0930

Intolerance Scores

• loftool: 0.850
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.380
• ghis: 0.385

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0458

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamts20
• Phenotype: limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary 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); pigmentation phenotype; embryo phenotype; cellular phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: proteolysis;positive regulation of signal transduction;extracellular matrix organization;negative regulation of apoptotic process;positive regulation of melanocyte differentiation
• Cellular component: extracellular space;collagen-containing extracellular matrix
• Molecular function: metalloendopeptidase activity;zinc ion binding