PRRC2A p.Ser1952=
c.5856C>G · rs769958324 · VCV3053226
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.21e-05%)
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 -0.13 | GERP -3.3, phastCons 0.46 |
| Overall | ||
| CADD | 5.083 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.21e-05%
Overall
6.21e-05%
1/1,609,288 alleles · very rare
exomes 1/1,457,042 · genomes 0/152,246 · joint denominator
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.Ser1952=
- Coding
- c.5856C>G
- MANE Select
- NM_004638
- dbSNP
- rs769958324
- Type
- single nucleotide variant
- Location
- chr6:31636530 (GRCh38)
- Gene constraint
- LOEUF 0.322 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 40.07
- Residue 1952
- the '3 x 50 aa type c repeats' 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-ser1952 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown