DST p.Ala7641=
c.22923G>A · rs554371778 · VCV3034202
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
Conditions
1
DST-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.043 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -5.3 | GERP -4.3 |
| Overall | ||
| CADD | 1.391 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,038 alleles
Filtering AF
0.00546%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00382%
Overall
0.00181%
29/1,605,658 alleles · ultra-rare
exomes 27/1,453,532 · genomes 2/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,038 |
| Admixed American | 0.0117% | 8,525 |
| European (non-Finnish) | 0.00162% | 61,806 |
| African / African-American | 0.00134% | 74,790 |
| South Asian | 0.00111% | 90,234 |
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.Ala7641=
- Coding
- c.22923G>A
- MANE Select
- NM_001374736
- dbSNP
- rs554371778
- Type
- single nucleotide variant
- Location
- chr6:56463601 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
Disease context
DST-related disorder
Similar variants
- DST p.Ala7641Val Uncertain significance ★ same residue
- DST p.Arg1696Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Gln1124Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Gln4226Ter Likely pathogenic ★ same condition
- DST p.Gln6260Ter Likely pathogenic ★ same condition
- DST p.Leu1891Ter Likely pathogenic ★ same condition
- DST c.16609-1G>T Conflicting classifications of pathogenicity ★ ⚠ same condition
- DST p.Tyr7662Cys Uncertain significance ★ 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/dst-p-ala7641 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown