PRODH p.Val50fs
c.148_157del · VCV3587838
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
2
hyperprolinemia type 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 14 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 8.7 | GERP 1, phastCons 1 |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PRODH
- Protein
- p.Val50fs
- Coding
- c.148_157del
- MANE Select
- NM_016335
- Type
- Deletion
- Location
- chr22:18936131 (GRCh38)
- Structure
- AlphaFold pLDDT 85.29
Disease context
hyperprolinemia type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: schizophrenia 4
For Hyperprolinemia type 1 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- All ages
Similar variants
- PRODH p.Glu153fs Pathogenic/Likely pathogenic ★★ same condition
- PRODH p.Thr44_Ala52del Uncertain significance ★★ same condition
- PRODH c.733-5del Benign/Likely benign ★★ same condition
- PRODH c.849+45del Benign ★★ same condition
- PRODH p.Leu108fs Pathogenic ★ same condition
- PRODH p.Leu393fs Likely pathogenic ★ same condition
- PRODH p.Ser323fs Pathogenic ★ same condition
- PRODH p.Val365fs 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/prodh-p-val50fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown