Is ADAMTS2 p.Ser939= (c.2817C>T) pathogenic?

ADAMTS2 p.Ser939= (c.2817C>T) is classified Conflicting classifications of pathogenicity in ADAMTS2 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-04-21). Ultra-rare (popmax 0.023%, nfe); Associated with Ehlers-Danlos syndrome.

What condition is associated with ADAMTS2 p.Ser939= (c.2817C>T)?

ADAMTS2 p.Ser939= (c.2817C>T) is associated with Ehlers-Danlos syndrome, Ehlers-Danlos syndrome, dermatosparaxis type (ClinVar).

How common is ADAMTS2 p.Ser939= (c.2817C>T) in the general population?

ADAMTS2 p.Ser939= (c.2817C>T) is ultra-rare (popmax 0.023%, nfe) (gnomAD).

ADAMTS2 p.Ser939=

c.2817C>T · rs201215425 · VCV353096

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.023%, nfe)

Conditions

Ehlers-Danlos syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -12	GERP -2.5
Overall
CADD	0.768	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.023% European (non-Finnish) · 271/1,179,922 alleles

Filtering AF 0.0207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0198%

Overall 0.0183% 295/1,612,846 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.023%	4,354
African / African-American	0.0133%	7,491
Remaining individualsnot grpmax-eligible	0.0112%	8,921
Admixed American	0.00833%	11,999
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,596
South Asian	0.0011%	91,082

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ADAMTS2
Protein: p.Ser939=
Coding: c.2817C>T
MANE Select: NM_014244
dbSNP: rs201215425
Type: single nucleotide variant
Location: chr5:179125114 (GRCh38)
Gene constraint: LOEUF 0.568 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 71.59
Residue 939: the tsp type-1 3 domain

Full ADAMTS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Ehlers-Danlos syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Ehlers-Danlos syndrome, dermatosparaxis type

Similar variants

ADAMTS2 c.2085+1G>T Likely pathogenic ★★ same condition
ADAMTS2 c.3088+1G>A Likely pathogenic ★★ same condition
ADAMTS2 c.688+1G>A Likely pathogenic ★★ same condition
ADAMTS2 c.688+2T>C Likely pathogenic ★★ same condition
ADAMTS2 p.Arg1030Ter Pathogenic/Likely pathogenic ★★ same condition
ADAMTS2 p.Arg980Ter Pathogenic/Likely pathogenic ★★ same condition
ADAMTS2 p.Cys659Ter Pathogenic/Likely pathogenic ★★ same condition
ADAMTS2 p.Gln225Ter Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/adamts2-p-ser939 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown