Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 8)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.93 | GERP -1.5, phastCons 0.007 |
| Regional constraint | o/e 0.12 | constrained · MANE · 23 kb · p 1.7e-05 · regional, not allelic |
| Overall | ||
| CADD | 7.654 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 8). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PRODH
- Protein
- p.Pro30Ser
- Coding
- c.88C>T
- MANE Select
- NM_016335
- dbSNP
- rs3815655
- Type
- single nucleotide variant
- Location
- chr22:18936200 (GRCh38)
- Structure
- AlphaFold pLDDT 85.29
- Residue 30
- a UniProt-annotated variant site (in)
Similar variants
- PRODH p.Pro30= Likely benign ★★ same residue
- PRODH p.Pro30His Uncertain significance ★ same residue
- PRODH c.1104+2T>C Likely pathogenic ★★ same condition
- PRODH p.Gln59Ter Pathogenic/Likely pathogenic ★★ same condition
- PRODH p.Tyr412Ter Pathogenic ★★ same condition
- PRODH c.1427+4C>T Uncertain significance ★★ same condition
- PRODH c.1615+1G>C Uncertain significance ★★ same condition
- PRODH c.482+6G>A Uncertain significance ★★ 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-pro30ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown