DPYD p.Pro86=
c.258G>A · rs201841475 · VCV788079
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0439%, sas)
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 -0.28 | GERP -2.9, phastCons 0.023 |
| Overall | ||
| CADD | 12.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0439%
South Asian · 40/91,060 alleles
Filtering AF
0.0331%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0293%
Overall
0.00632%
102/1,612,980 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0439% | 2,276 |
| Middle Eastern | 0.033% | 3,026 |
| Admixed American | 0.0183% | 5,453 |
| African / African-American | 0.016% | 6,249 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,412 |
| East Asian | 0.00446% | 22,406 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,570 |
| European (non-Finnish) | 0.00237% | 42,122 |
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.Pro86=
- Coding
- c.258G>A
- MANE Select
- NM_000110
- dbSNP
- rs201841475
- Type
- single nucleotide variant
- Location
- chr1:97740455 (GRCh38)
- Gene constraint
- LOEUF 1.09 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.23
- Residue 86
- the 4fe-4s ferredoxin-type 1 domain
Similar variants
- DPYD p.Pro86Leu Pathogenic/Likely pathogenic ★★ same residue
- DPYD c.1340-2A>C Likely pathogenic ★★ same type
- DPYD c.1905+1G>C Pathogenic/Likely pathogenic ★★ same type
- DPYD c.233+1G>T Likely pathogenic ★★ same type
- DPYD c.2622+1G>A Likely pathogenic ★★ same type
- DPYD c.2767-1G>A Likely pathogenic ★★ same type
- DPYD c.680+1G>T Likely pathogenic ★★ same type
- DPYD p.Arg21Ter Pathogenic/Likely pathogenic ★★ 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/dpyd-p-pro86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown