PRRC2A p.Pro1167=
c.3501A>G · rs146502735 · VCV3049046
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.233%, afr)
Conditions
1
PRRC2A-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.186 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7.3 | GERP -3.5 |
| Overall | ||
| CADD | 0.135 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.233%
African / African-American · 172/73,926 alleles
Filtering AF
0.204%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.193%
Overall
0.0148%
235/1,590,668 alleles · rare
exomes 138/1,439,134 · genomes 97/151,534 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.233% | 430 |
| Admixed American | 0.0212% | 4,706 |
| Remaining individualsnot grpmax-eligible | 0.0163% | 6,137 |
| European (non-Finnish) | 0.00351% | 28,515 |
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
- PRRC2A
- Protein
- p.Pro1167=
- Coding
- c.3501A>G
- MANE Select
- NM_004638
- dbSNP
- rs146502735
- Type
- single nucleotide variant
- Location
- chr6:31632174 (GRCh38)
- Gene constraint
- LOEUF 0.322 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 40.07
- Residue 1167
- the '4 x 57 aa type a repeats' region; the 'disordered' region
Disease context
PRRC2A-related disorder
Similar variants
- PRRC2A p.Lys308Arg Uncertain significance ⚠ same condition
- PRRC2A c.391-6C>A Likely benign same condition
- PRRC2A c.4720-6C>G Likely benign same condition
- PRRC2A c.5624+9C>T Benign same condition
- PRRC2A c.760-10C>G Likely benign same condition
- PRRC2A c.*9C>T Likely benign same condition
- PRRC2A p.Ala1222= Likely benign same condition
- PRRC2A p.Ala1283Thr Benign 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/prrc2a-p-pro1167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown