DSTYK p.Arg488=
c.1464G>A · rs549617235 · VCV2964998
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -5.4 | GERP -4.6 |
| Overall | ||
| CADD | 0.133 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000743%
12/1,614,022 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| Admixed American | 0.00167% | 59,998 |
| African / African-American | 0.00134% | 74,906 |
| European (non-Finnish) | 0.000508% | 196,671 |
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.Arg488=
- Coding
- c.1464G>A
- MANE Select
- NM_015375
- dbSNP
- rs549617235
- Type
- single nucleotide variant
- Location
- chr1:205163816 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02
- Residue 488
- 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-arg488 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown