PRRC2C p.Ala2162Pro
c.6484G>C · rs776298228 · VCV2529088
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.131%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.078 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP -0.72, phastCons 1 |
| Regional constraint | o/e 0.95 | unconstrained · MANE · 21 kb · p 0.17 · regional, not allelic |
| Overall | ||
| CADD | 20.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.131%
Middle Eastern · 8/6,084 alleles
Filtering AF
0.0654%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0477%
Overall
0.0125%
201/1,613,674 alleles · rare
exomes 192/1,461,480 · genomes 9/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.131% | 761 |
| European (non-Finnish) | 0.0152% | 6,591 |
| Finnishnot grpmax-eligible | 0.00781% | 12,802 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,801 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,613 |
| Admixed American | 0.00334% | 29,980 |
| African / African-American | 0.00133% | 74,934 |
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
- PRRC2C
- Protein
- p.Ala2162Pro
- Coding
- c.6484G>C
- MANE Select
- NM_001387844
- dbSNP
- rs776298228
- Type
- single nucleotide variant
- Location
- chr1:171566769 (GRCh38)
- Gene constraint
- LOEUF 0.287 · pLI 1.00 (gnomAD)
- Residue 2162
- the 'disordered' region
Similar variants
- PRRC2C c.1055+2T>C Uncertain significance ★ same type
- PRRC2C p.Ala104Thr Uncertain significance ★ same type
- PRRC2C p.Ala1120Thr Uncertain significance ★ same type
- PRRC2C p.Ala1762Ser Uncertain significance ★ same type
- PRRC2C p.Ala1774Ser Uncertain significance ★ same type
- PRRC2C p.Ala1785Val Uncertain significance ★ same type
- PRRC2C p.Ala1927Thr Uncertain significance ★ same type
- PRRC2C p.Ala1930Val 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/prrc2c-p-ala2162pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown