ADAMTS2 p.Cys1093=
c.3279T>C · rs73806887 · VCV517917
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.5%, afr)
Conditions
2
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 0.015 | GERP -3.8, phastCons 0.053 |
| Overall | ||
| CADD | 8.667 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.5%
African / African-American · 1,879/75,030 alleles
Filtering AF
2.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.37%
Overall
0.134%
2,162/1,613,802 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.5% | 40 |
| Remaining individualsnot grpmax-eligible | 0.19% | 525 |
| Admixed American | 0.158% | 632 |
| Middle Eastern | 0.066% | 1,515 |
| South Asian | 0.00879% | 11,381 |
| European (non-Finnish) | 0.00483% | 20,698 |
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.Cys1093=
- Coding
- c.3279T>C
- MANE Select
- NM_014244
- dbSNP
- rs73806887
- Type
- single nucleotide variant
- Location
- chr5:179114224 (GRCh38)
- Gene constraint
- LOEUF 0.568 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 71.59
- Residue 1093
- the plac domain
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-cys1093 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown