PRRC2A p.Phe1584=
c.4752C>T · rs146122581 · VCV3041196
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.184%, 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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.14 | GERP 0.57, phastCons 0.87 |
| Overall | ||
| CADD | 9.186 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.184%
African / African-American · 135/73,316 alleles
Filtering AF
0.159%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.149%
Overall
0.00852%
136/1,596,410 alleles · rare
exomes 47/1,444,168 · genomes 89/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.184% | 543 |
| Admixed American | 0.00187% | 53,556 |
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.Phe1584=
- Coding
- c.4752C>T
- MANE Select
- NM_004638
- dbSNP
- rs146122581
- Type
- single nucleotide variant
- Location
- chr6:31634268 (GRCh38)
- Gene constraint
- LOEUF 0.322 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 40.07
- Residue 1584
- 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-phe1584 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown