DSTYK p.Glu403=
c.1209A>G · rs35208779 · VCV716060
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3%, afr)
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 -2.9 | GERP -2.5 |
| Overall | ||
| CADD | 3.108 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3%
African / African-American · 2,252/75,002 alleles
Filtering AF
2.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.86%
Overall
0.157%
2,541/1,614,070 alleles · low-frequency
exomes 1,261/1,461,844 · genomes 1,280/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3% | 33 |
| Remaining individualsnot grpmax-eligible | 0.25% | 401 |
| Admixed American | 0.107% | 938 |
| Middle Eastern | 0.066% | 1,516 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,974 |
| South Asian | 0.00878% | 11,384 |
| European (non-Finnish) | 0.00347% | 28,780 |
| East Asian | 0.00223% | 44,884 |
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
- DSTYK
- Protein
- p.Glu403=
- Coding
- c.1209A>G
- MANE Select
- NM_015375
- dbSNP
- rs35208779
- Type
- single nucleotide variant
- Location
- chr1:205169278 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02
- Residue 403
- a UniProt-annotated variant site (in cakut1; uncertain significance)
Similar variants
- DSTYK p.Ala206Val Uncertain significance ★★ ⚠ same type
- DSTYK p.Ala477Ser Uncertain significance ★★ same type
- DSTYK p.Ala601Val Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg411Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg462Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg471Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg626Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg635His 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/dstyk-p-glu403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown