DST p.Arg6697His
c.20090G>A · rs1224386090 · VCV1360195
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00447%, eas)
Conditions
3
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.111 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.37 | GERP -1.8, phastCons 0.98 |
| Regional constraint | o/e 0.83 | unconstrained · MANE · 46 kb · p 3.7e-11 · regional, not allelic |
| Overall | ||
| CADD | 20.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00447%
East Asian · 2/44,740 alleles
Filtering AF
0.000741%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000476%
Overall
0.00103%
15/1,453,166 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00447% | 22,370 |
| European (non-Finnish) | 0.00111% | 90,410 |
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.Arg6697His
- Coding
- c.20090G>A
- MANE Select
- NM_001374736
- dbSNP
- rs1224386090
- Type
- single nucleotide variant
- Location
- chr6:56497860 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
Similar variants
- DST p.Arg6697Cys Uncertain significance ★ same residue
- DST c.22959+1G>A Likely pathogenic ★★ same condition
- DST p.Arg1512Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Arg1696Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Arg22Ter Likely pathogenic ★★ same condition
- DST p.Arg7329Ter Pathogenic ★★ same condition
- DST p.Cys1828Ter Pathogenic/Likely pathogenic ★★ same condition
- DST p.Gln1124Ter Pathogenic/Likely 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/dst-p-arg6697his (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown