DSTYK p.Arg462=
c.1384C>A · rs77626160 · VCV1547372
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.75%, sas)
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 5.1 | GERP 0.42, phastCons 1 |
| Overall | ||
| CADD | 9.748 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.75%
South Asian · 2,503/91,056 alleles
Filtering AF
2.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.62%
Overall
0.995%
16,054/1,614,048 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.75% | 36 |
| Middle Eastern | 1.58% | 63 |
| European (non-Finnish) | 0.996% | 100 |
| Remaining individualsnot grpmax-eligible | 0.921% | 109 |
| Ashkenazi Jewishnot grpmax-eligible | 0.888% | 113 |
| Amishnot grpmax-eligible | 0.877% | 114 |
| Admixed American | 0.595% | 168 |
| Finnishnot grpmax-eligible | 0.587% | 170 |
| African / African-American | 0.165% | 605 |
| East Asian | 0.00891% | 11,220 |
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.Arg462=
- Coding
- c.1384C>A
- MANE Select
- NM_015375
- dbSNP
- rs77626160
- Type
- single nucleotide variant
- Location
- chr1:205163896 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02
- Residue 462
- a UniProt-annotated variant site (in cakut1; uncertain significance)
Similar variants
- DSTYK p.Arg462Gln Uncertain significance ★★ ⚠ same residue
- DSTYK p.Arg462Ter Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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.Arg471Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg626Gln 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-arg462 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown