ADAMTS2

ADAM metallopeptidase with thrombospondin type 1 motif 2, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Basic information

Region (hg38): 5:179110853-179345461

Links

ENSG00000087116 ∙ NCBI:9509 ∙ OMIM:604539 ∙ HGNC:218 ∙ Uniprot:O95450 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Ehlers-Danlos syndrome, dermatosparaxis type (Definitive), mode of inheritance: AR
• Ehlers-Danlos syndrome, dermatosparaxis type (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, dermatosparaxis type (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, dermatosparaxis type (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, dermatosparaxis type (Supportive), mode of inheritance: AR
• Ehlers-Danlos syndrome, dermatosparaxis type (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ehlers-Danlos syndrome, dermatosparaxis type	AR	Obstetric	Individuals may be prone to injuries (especially during delivery, as multiple congenital skull fractures and intracranial hemorrhage have been reported), and knowledge may allow delivery-based interventions to decrease related morbidity and mortality	Craniofacial; Dermatologic; Musculoskeletal; Obstetric	1303238; 8215497; 7735500; 10417273; 15373769; 15389701; 18973246

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS2 gene.

• Ehlers-Danlos syndrome, dermatosparaxis type (44 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS2 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			3	573	14	590
missense		1	417	13	5	436
nonsense	17	10	3			30
start loss		1				1
frameshift	27	30	4			61
inframe indel			31	1	1	33
splice donor/acceptor (+/-2bp)		15			1	16
splice region			18	90	2	110
non coding			49	281	88	418
Total	44	57	507	868	109

Highest pathogenic variant AF is 0.0000526

Variants in ADAMTS2

This is a list of pathogenic ClinVar variants found in the ADAMTS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-179110915-A-T		Ehlers-Danlos syndrome, dermatosparaxis type	Benign (Jan 12, 2018)
5-179110915-AC-TT		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jun 14, 2016)
5-179110916-C-T		Ehlers-Danlos syndrome, dermatosparaxis type	Benign (Jan 13, 2018)
5-179110938-GGTT-G		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jun 14, 2016)
5-179110949-C-T		Ehlers-Danlos syndrome, dermatosparaxis type	Benign (Jan 13, 2018)
5-179111013-A-G		Ehlers-Danlos syndrome, dermatosparaxis type	Likely benign (Jul 08, 2024)
5-179111014-C-T		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 13, 2018)
5-179111027-A-C		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 12, 2018)
5-179111047-G-T		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 13, 2018)
5-179111143-T-C		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 13, 2018)
5-179111269-T-C		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 13, 2018)
5-179111272-G-A		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 13, 2018)
5-179111278-A-C		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 12, 2018)
5-179111280-A-G		Ehlers-Danlos syndrome, dermatosparaxis type	Likely benign (Jan 13, 2018)
5-179111356-G-T		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 13, 2018)
5-179111427-C-T		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 13, 2018)
5-179111428-G-A		Ehlers-Danlos syndrome, dermatosparaxis type	Benign (Jan 13, 2018)
5-179111447-T-C		Ehlers-Danlos syndrome, dermatosparaxis type	Likely benign (Jan 13, 2018)
5-179111470-C-T		Ehlers-Danlos syndrome, dermatosparaxis type	Likely benign (Jan 12, 2018)
5-179111471-G-A		Ehlers-Danlos syndrome, dermatosparaxis type	Benign (Jan 13, 2018)
5-179111565-G-A		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (May 17, 2018)
5-179111566-G-A		Ehlers-Danlos syndrome, dermatosparaxis type	Benign (Jan 12, 2018)
5-179111597-G-A		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 12, 2018)
5-179111671-A-T		Ehlers-Danlos syndrome, dermatosparaxis type	Likely benign (Apr 27, 2017)
5-179111687-G-T		Ehlers-Danlos syndrome, dermatosparaxis type	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS2	protein_coding	protein_coding	ENST00000251582	22	234580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.966	0.0339	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	637	747	0.853	0.0000518	7846
Missense in Polyphen		212	326.2	0.64991		3393
Synonymous	-0.390	320	311	1.03	0.0000233	2391
Loss of Function	5.59	10	54.6	0.183	0.00000275	617

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00299	0.00298
East Asian	0.000278	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.000278	0.000272
South Asian	0.000361	0.000359
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves the propeptides of type I and II collagen prior to fibril assembly. Does not act on type III collagen. May also play a role in development that is independent of its role in collagen biosynthesis.
• Disease: DISEASE: Ehlers-Danlos syndrome, dermatosparaxis type (EDSDERMS) [MIM:225410]: A form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. EDSDERMS is an autosomal recessive form characterized by extreme skin fragility and easy bruising, large fontanels, blue sclerae, puffy eyelids, micrognathia, umbilical hernia, and short fingers. Joint hypermobility becomes more important with age. {ECO:0000269|PubMed:10417273}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Collagen biosynthesis and modifying enzymes;Post-translational protein modification;Metabolism of proteins;Collagen formation;Extracellular matrix organization;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.315

Intolerance Scores

• loftool: 0.135
• rvis_EVS: -1.8
• rvis_percentile_EVS: 2.22

Haploinsufficiency Scores

• pHI: 0.333
• hipred: Y
• hipred_score: 0.685
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.213

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamts2
• 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; craniofacial phenotype; reproductive system phenotype; normal phenotype; respiratory system phenotype; skeleton phenotype

Gene ontology

• Biological process: spermatogenesis;protein processing;collagen fibril organization;lung development;collagen catabolic process;skin development
• Cellular component: extracellular region;collagen-containing extracellular matrix
• Molecular function: metalloendopeptidase activity;metallopeptidase activity;zinc ion binding