PARP3 p.Pro479=
c.1437G>A · VCV4836676
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00891%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -2.4 |
| Overall | ||
| CADD | 3.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,878 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.00273%
44/1,613,426 alleles · very rare
exomes 39/1,461,084 · genomes 5/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,220 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,227 |
| European (non-Finnish) | 0.00305% | 32,767 |
| African / African-American | 0.00266% | 37,530 |
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
- PARP3
- Protein
- p.Pro479=
- Coding
- c.1437G>A
- MANE Select
- NM_001003931
- Type
- single nucleotide variant
- Location
- chr3:51948315 (GRCh38)
- Gene constraint
- LOEUF 1.001 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.68 · 16 PDB
- Residue 479
- the parp catalytic domain; the 'disordered' region; an α-helix
Similar variants
- PARP3 p.Pro479Arg Uncertain significance ★ ⚠ same residue
- PARP3 p.Ala41Ser Benign ★★ same type
- PARP3 p.Arg47= Benign ★★ same type
- PARP3 p.Gly385Ser Benign ★★ ⚠ same type
- PARP3 p.Ile153= Likely benign ★★ same type
- PARP3 p.Ala227Thr Uncertain significance ★ ⚠ same type
- PARP3 p.Ala290Val Uncertain significance ★ ⚠ same type
- PARP3 p.Ala295Asp 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/parp3-p-pro479 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown