PRRC2A p.Arg904=
c.2712C>A · rs116345584 · VCV3044248
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.35%, afr)
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 -11 | GERP -3.1 |
| Overall | ||
| CADD | 0.006 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.35%
African / African-American · 1,008/74,616 alleles
Filtering AF
1.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.25%
Overall
0.203%
3,254/1,606,032 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.35% | 74 |
| Ashkenazi Jewishnot grpmax-eligible | 0.926% | 108 |
| Admixed American | 0.552% | 181 |
| Middle Eastern | 0.515% | 194 |
| Remaining individualsnot grpmax-eligible | 0.406% | 246 |
| European (non-Finnish) | 0.115% | 872 |
| Finnishnot grpmax-eligible | 0.0175% | 5,703 |
| South Asian | 0.0122% | 8,209 |
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.Arg904=
- Coding
- c.2712C>A
- MANE Select
- NM_004638
- dbSNP
- rs116345584
- Type
- single nucleotide variant
- Location
- chr6:31631385 (GRCh38)
- Gene constraint
- LOEUF 0.322 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 40.07
- Residue 904
- the '4 x 57 aa type a repeats' region; the 'disordered' region; a modified residue (omega-n-methylarginine)
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-arg904 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown