DPYS p.Val497=
c.1491C>T · rs561593514 · VCV2958801
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 -1.2 | GERP -3.8 |
| Overall | ||
| CADD | 2.609 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,878 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000991%
16/1,614,114 alleles · very rare
exomes 15/1,461,856 · genomes 1/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,959 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,836 |
| African / African-American | 0.004% | 25,008 |
| South Asian | 0.0022% | 45,534 |
| European (non-Finnish) | 0.000424% | 236,003 |
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
- DPYS
- Protein
- p.Val497=
- Coding
- c.1491C>T
- MANE Select
- NM_001385
- dbSNP
- rs561593514
- Type
- single nucleotide variant
- Location
- chr8:104381267 (GRCh38)
- Gene constraint
- LOEUF 1.029 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.00 · 1 PDB
Similar variants
- DPYS c.424-1G>A Pathogenic/Likely pathogenic ★★ same type
- DPYS p.Arg302Gln Likely pathogenic ★★ same type
- DPYS p.Arg302Ter Pathogenic/Likely pathogenic ★★ same type
- DPYS p.Arg465Ter Pathogenic ★★ same type
- DPYS p.Arg475Ter Pathogenic/Likely pathogenic ★★ same type
- DPYS p.Arg490Cys Pathogenic/Likely pathogenic ★★ same type
- DPYS p.Arg490His Pathogenic/Likely pathogenic ★★ same type
- DPYS p.Gln190Ter 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/dpys-p-val497 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown