DST p.Ala86=
c.258A>G · rs201106926 · VCV1284715
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.28%, nfe)
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 -4.2 | GERP -2.9 |
| Overall | ||
| CADD | 1.136 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.28%
European (non-Finnish) · 2,863/1,021,848 alleles
Filtering AF
0.272%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.268%
Overall
0.222%
3,042/1,367,684 alleles · rare
exomes 2,873/1,215,394 · genomes 169/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.28% | 357 |
| Remaining individualsnot grpmax-eligible | 0.226% | 443 |
| Middle Eastern | 0.189% | 530 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0589% | 1,697 |
| African / African-American | 0.0354% | 2,827 |
| Finnishnot grpmax-eligible | 0.0347% | 2,880 |
| Admixed American | 0.0228% | 4,383 |
| South Asian | 0.00341% | 29,351 |
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
- DST
- Protein
- p.Ala86=
- Coding
- c.258A>G
- MANE Select
- NM_001374736
- dbSNP
- rs201106926
- Type
- single nucleotide variant
- Location
- chr6:56900580 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
- Residue 86
- the calponin-homology (ch) 1 domain; the 'actin-binding' region
Similar variants
- DST p.Ala86Gly Uncertain significance ★ same residue
- DST c.22959+1G>A Likely pathogenic ★★ same type
- DST p.Arg1512Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Arg1696Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Arg22Ter Likely pathogenic ★★ same type
- DST p.Arg7329Ter Pathogenic ★★ same type
- DST p.Cys1828Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Gln1124Ter Pathogenic/Likely pathogenic ★★ 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/dst-p-ala86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown