PRRC2A p.Ser1954=
c.5862G>A · VCV3355698
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.37 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.97 | GERP -3.8 |
| Overall | ||
| CADD | 10.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,864 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000313%
Overall
0.000746%
12/1,608,948 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,864 |
| African / African-American | 0.00134% | 74,594 |
| European (non-Finnish) | 0.000849% | 117,821 |
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.Ser1954=
- Coding
- c.5862G>A
- MANE Select
- NM_004638
- Type
- single nucleotide variant
- Location
- chr6:31636536 (GRCh38)
- Gene constraint
- LOEUF 0.322 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 40.07
- Residue 1954
- the '3 x 50 aa type c repeats' region
Disease context
PRRC2A-related disorder
Similar variants
- PRRC2A p.Ser1954Leu 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-ser1954 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown