DSTYK p.Arg40=
c.120G>T · rs201374829 · VCV780090
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.1%, eas)
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 -1.1 | GERP -3.9, phastCons 0.001 |
| Overall | ||
| CADD | 10.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.1%
East Asian · 492/44,784 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.987%
Overall
0.0506%
814/1,610,176 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.1% | 91 |
| South Asian | 0.291% | 344 |
| Remaining individualsnot grpmax-eligible | 0.0737% | 1,356 |
| Middle Eastern | 0.0496% | 2,018 |
| Admixed American | 0.00835% | 11,970 |
| African / African-American | 0.00133% | 74,912 |
| European (non-Finnish) | 0.000254% | 393,045 |
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.Arg40=
- Coding
- c.120G>T
- MANE Select
- NM_015375
- dbSNP
- rs201374829
- Type
- single nucleotide variant
- Location
- chr1:205211416 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02
- Residue 40
- a UniProt-annotated variant site (in cakut1; uncertain significance)
Similar variants
- DSTYK p.Arg40Gly 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-arg40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown