QDPR p.Val80=
c.240G>A · rs2474675147 · VCV2131254
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
dihydropteridine reductase deficiency
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.42 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.43 | gain · loss 0.17 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 16.31 | 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
- QDPR
- Protein
- p.Val80=
- Coding
- c.240G>A
- MANE Select
- NM_000320
- dbSNP
- rs2474675147
- Type
- single nucleotide variant
- Location
- chr4:17504434 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.43 · 2 PDB
- Residue 80
- a β-strand
Disease context
dihydropteridine reductase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hyperphenylalaninemia due to tetrahydrobiopterin deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Japan)
Similar variants
- QDPR c.436+2552A>G Pathogenic ★★ same condition
- QDPR c.545+1G>A Pathogenic ★★ same condition
- QDPR c.546-1G>A Likely pathogenic ★★ same condition
- QDPR p.Arg221Ter Pathogenic ★★ same condition
- QDPR p.His158Tyr Pathogenic/Likely pathogenic ★★ same condition
- QDPR p.Phe212Ser Likely pathogenic ★★ same condition
- QDPR p.Ser115Leu Pathogenic/Likely pathogenic ★★ same condition
- QDPR p.Tyr150Cys Pathogenic ★★ 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/qdpr-p-val80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown