DPYD p.Arg561=
c.1683A>C · rs1648178154 · VCV1777949
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.19 | GERP -4.3, phastCons 0.66 |
| Overall | ||
| CADD | 7.286 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DPYD
- Protein
- p.Arg561=
- Coding
- c.1683A>C
- MANE Select
- NM_000110
- dbSNP
- rs1648178154
- Type
- single nucleotide variant
- Location
- chr1:97515783 (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.Arg561Ter Pathogenic/Likely pathogenic ★★ same residue
- 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
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-arg561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown