DPYD p.Ser534=
c.1602T>C · rs1257539978 · VCV2567625
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000509%, nfe)
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 0.45 | GERP -4.6, phastCons 0.77 |
| Overall | ||
| CADD | 5.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000509%
European (non-Finnish) · 6/1,179,244 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000411%
6/1,460,830 alleles · very rare
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.Ser534=
- Coding
- c.1602T>C
- MANE Select
- NM_000110
- dbSNP
- rs1257539978
- Type
- single nucleotide variant
- Location
- chr1:97515864 (GRCh38)
- Gene constraint
- LOEUF 1.09 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.23
- Residue 534
- a UniProt-annotated variant site (in allele dpyd*4)
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-ser534 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown