PRODH p.Val365Phe
c.1093G>T · rs768237039 · VCV2582999
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0474%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.206 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -8.8 | GERP -4.3 |
| Regional constraint | o/e 0.12 | constrained · MANE · 23 kb · p 1.7e-05 · regional, not allelic |
| Overall | ||
| CADD | 12.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0474%
South Asian · 1/2,110 alleles
Overall
0.00837%
1/11,944 alleles · ultra-rare
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
- PRODH
- Protein
- p.Val365Phe
- Coding
- c.1093G>T
- MANE Select
- NM_016335
- dbSNP
- rs768237039
- Type
- single nucleotide variant
- Location
- chr22:18919717 (GRCh38)
- Structure
- AlphaFold pLDDT 85.29
Similar variants
- PRODH p.Val365Ile Uncertain significance ★★ same residue
- PRODH p.Val365= Uncertain significance ★ same residue
- PRODH p.Val365fs Pathogenic ★ same residue
- PRODH c.1104+2T>C Likely pathogenic ★★ same type
- PRODH p.Gln59Ter Pathogenic/Likely pathogenic ★★ same type
- PRODH p.Tyr412Ter Pathogenic ★★ same type
- PRODH c.1427+4C>T Uncertain significance ★★ same type
- PRODH c.1615+1G>C Uncertain significance ★★ 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/prodh-p-val365phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown