ADAMTS10 p.Asp403=
c.1209C>T · rs554222679 · VCV1991690
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 -4.1 |
| Overall | ||
| CADD | 4.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,086 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000682%
11/1,613,996 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,772 |
| African / African-American | 0.00133% | 75,050 |
| European (non-Finnish) | 0.000508% | 196,669 |
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
- ADAMTS10
- Protein
- p.Asp403=
- Coding
- c.1209C>T
- MANE Select
- NM_030957
- dbSNP
- rs554222679
- Type
- single nucleotide variant
- Location
- chr19:8596201 (GRCh38)
- Gene constraint
- LOEUF 0.467 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.88
- Residue 403
- a disulfide bond; the peptidase m12b domain
Similar variants
- ADAMTS10 c.810+1G>A Likely pathogenic ★★ same type
- ADAMTS10 p.Arg237Ter Pathogenic ★★ same type
- ADAMTS10 c.1337+3G>T Uncertain significance ★★ same type
- ADAMTS10 c.1587+6C>A Uncertain significance ★★ same type
- ADAMTS10 c.894+5G>A Uncertain significance ★★ same type
- ADAMTS10 c.-99-3C>T Uncertain significance ★★ same type
- ADAMTS10 p.Ala13Thr Uncertain significance ★★ ⚠ same type
- ADAMTS10 p.Ala247Ser Uncertain significance ★★ ⚠ same type
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/adamts10-p-asp403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown