DPYS p.Leu311=
c.933C>T · rs767671230 · VCV1968759
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | donor loss, 17 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 5.016 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,078 alleles
Overall
0.000137%
2/1,461,826 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,078 |
| European (non-Finnish) | 8.47e-05% | 1,180,002 |
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.Leu311=
- Coding
- c.933C>T
- MANE Select
- NM_001385
- dbSNP
- rs767671230
- Type
- single nucleotide variant
- Location
- chr8:104429562 (GRCh38)
- Gene constraint
- LOEUF 1.029 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.00 · 1 PDB
- Residue 311
- an α-helix
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-leu311 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown