DSTYK p.Gly20=
c.60C>G · rs373353993 · VCV2056160
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.388%, 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 3.4 | GERP 0.46, phastCons 1 |
| Overall | ||
| CADD | 10.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.388%
Middle Eastern · 23/5,922 alleles
Filtering AF
0.265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.225%
Overall
0.0588%
931/1,584,402 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.388% | 257 |
| Ashkenazi Jewishnot grpmax-eligible | 0.138% | 724 |
| Remaining individualsnot grpmax-eligible | 0.101% | 990 |
| Admixed American | 0.0828% | 1,208 |
| European (non-Finnish) | 0.0629% | 1,589 |
| African / African-American | 0.0149% | 6,719 |
| South Asian | 0.0113% | 8,841 |
| Finnishnot grpmax-eligible | 0.00186% | 53,828 |
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.Gly20=
- Coding
- c.60C>G
- MANE Select
- NM_015375
- dbSNP
- rs373353993
- Type
- single nucleotide variant
- Location
- chr1:205211476 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02
- Residue 20
- a UniProt-annotated variant site (in cakut1; uncertain significance); the 'disordered' region
Similar variants
- DSTYK p.Gly20Asp Uncertain significance ★ ⚠ 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.Arg462Gln 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-gly20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown