DCST1 p.Tyr362=
c.1086C>T · rs146174361 · VCV789152
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.931%, nfe)
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 -11 | GERP -2.2 |
| Overall | ||
| CADD | 0.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.931%
European (non-Finnish) · 10,976/1,178,332 alleles
Filtering AF
0.917%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.911%
Overall
0.781%
12,592/1,611,472 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.931% | 107 |
| South Asian | 0.86% | 116 |
| Remaining individualsnot grpmax-eligible | 0.762% | 131 |
| Admixed American | 0.209% | 480 |
| Middle Eastern | 0.167% | 600 |
| Finnishnot grpmax-eligible | 0.156% | 640 |
| African / African-American | 0.148% | 676 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0276% | 3,626 |
| East Asian | 0.00891% | 11,218 |
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
- DCST1
- Protein
- p.Tyr362=
- Coding
- c.1086C>T
- MANE Select
- NM_152494
- dbSNP
- rs146174361
- Type
- single nucleotide variant
- Location
- chr1:155043423 (GRCh38)
- Gene constraint
- LOEUF 1.032 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.35
Similar variants
- DCST1 p.Ala199Val Benign ★★ same type
- DCST1 p.Thr158Ile Benign ★★ ⚠ same type
- DCST1 p.Ala103Thr Uncertain significance ★ ⚠ same type
- DCST1 p.Ala124Pro Uncertain significance ★ ⚠ same type
- DCST1 p.Ala124Thr Uncertain significance ★ ⚠ same type
- DCST1 p.Ala219Val Uncertain significance ★ ⚠ same type
- DCST1 p.Ala391Ser Uncertain significance ★ ⚠ same type
- DCST1 p.Ala450Ser 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/dcst1-p-tyr362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown