DPYD p.Phe158=
c.474T>C · rs190771411 · VCV298301
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.208%, eas)
Conditions
1
Inborn genetic diseases
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 0.59 | GERP 0.46, phastCons 0.87 |
| Overall | ||
| CADD | 8.092 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.208%
East Asian · 93/44,798 alleles
Filtering AF
0.173%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.161%
Overall
0.0059%
95/1,611,352 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.208% | 482 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,366 |
| European (non-Finnish) | 8.49e-05% | 1,178,080 |
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
- DPYD
- Protein
- p.Phe158=
- Coding
- c.474T>C
- MANE Select
- NM_000110
- dbSNP
- rs190771411
- Type
- single nucleotide variant
- Location
- chr1:97721519 (GRCh38)
- Gene constraint
- LOEUF 1.09 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.23
Similar variants
- DPYD p.Ala513Val Uncertain significance ★★ ⚠ same condition
- DPYD p.Ala664Ser Uncertain significance ★★ ⚠ same condition
- DPYD p.Arg332Gln Uncertain significance ★★ ⚠ same condition
- DPYD p.Arg410Gln Uncertain significance ★★ ⚠ same condition
- DPYD p.Arg692Gln Uncertain significance ★★ ⚠ same condition
- DPYD p.Gln508= Uncertain significance ★★ same condition
- DPYD p.Glu13Lys Uncertain significance ★★ ⚠ same condition
- DPYD p.Glu950Lys Uncertain significance ★★ ⚠ same condition
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/dpyd-p-phe158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown