PRRC2A p.Pro2057=
c.6171G>A · rs3817659 · VCV3041516
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.98%, eas)
Conditions
1
PRRC2A-related disorder
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 0.2 | GERP -1.8, phastCons 0.92 |
| Overall | ||
| CADD | 8.518 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.98%
East Asian · 1,785/44,842 alleles
Filtering AF
3.83%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.76%
Overall
0.306%
4,920/1,608,542 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.98% | 25 |
| African / African-American | 2.43% | 41 |
| Middle Eastern | 0.564% | 177 |
| Admixed American | 0.345% | 290 |
| Remaining individualsnot grpmax-eligible | 0.278% | 360 |
| Ashkenazi Jewishnot grpmax-eligible | 0.232% | 430 |
| South Asian | 0.132% | 760 |
| European (non-Finnish) | 0.06% | 1,666 |
| Finnishnot grpmax-eligible | 0.0127% | 7,852 |
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.Pro2057=
- Coding
- c.6171G>A
- MANE Select
- NM_004638
- dbSNP
- rs3817659
- Type
- single nucleotide variant
- Location
- chr6:31637065 (GRCh38)
- Gene constraint
- LOEUF 0.322 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 40.07
- Residue 2057
- the '3 x 50 aa type c repeats' region
Disease context
PRRC2A-related disorder
Similar variants
- PRRC2A p.Pro2057Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro2057 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown