DST p.Arg6697Cys
c.20089C>T · rs778539752 · VCV1771088
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0331%, mid)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.246 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.6 | GERP 2.4, phastCons 1 |
| Regional constraint | o/e 0.83 | unconstrained · MANE · 46 kb · p 3.7e-11 · regional, not allelic |
| Overall | ||
| CADD | 25.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0331%
Middle Eastern · 2/6,038 alleles
Filtering AF
0.0082%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00636%
Overall
0.00243%
39/1,605,408 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0331% | 3,019 |
| African / African-American | 0.0148% | 6,774 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,528 |
| East Asian | 0.00447% | 22,368 |
| Admixed American | 0.00169% | 59,074 |
| European (non-Finnish) | 0.00153% | 65,299 |
| South Asian | 0.00112% | 89,556 |
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.Arg6697Cys
- Coding
- c.20089C>T
- MANE Select
- NM_001374736
- dbSNP
- rs778539752
- Type
- single nucleotide variant
- Location
- chr6:56497861 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
Similar variants
- DST p.Arg6697His Uncertain significance ★★ same residue
- DST p.Gln4023Ter Pathogenic/Likely pathogenic ★★ same condition
- DST c.16770+5T>C Uncertain significance ★★ same condition
- DST c.17269-3T>A Uncertain significance ★★ same condition
- DST c.18129+3A>G Uncertain significance ★★ same condition
- DST c.182-5C>T Uncertain significance ★★ same condition
- DST c.19896+4C>T Uncertain significance ★★ same condition
- DST c.20551-3A>C 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-arg6697cys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown