PRRC2C p.Pro118Ser
c.352C>T · VCV4145545
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0363%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.052 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 1.19 | unconstrained · MANE · 7,677 bp · p 0.0079 · regional, not allelic |
| Overall | ||
| CADD | 23.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0363%
Admixed American · 19/52,316 alleles
Filtering AF
0.0237%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00141%
22/1,562,144 alleles · ultra-rare
exomes 19/1,410,100 · genomes 3/152,044 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0363% | 2,753 |
| Middle Eastern | 0.0166% | 6,032 |
| South Asian | 0.00118% | 84,548 |
| European (non-Finnish) | 8.67e-05% | 1,153,309 |
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
- PRRC2C
- Protein
- p.Pro118Ser
- Coding
- c.352C>T
- MANE Select
- NM_001387844
- Type
- single nucleotide variant
- Location
- chr1:171514597 (GRCh38)
- Gene constraint
- LOEUF 0.287 · pLI 1.00 (gnomAD)
- Residue 118
- the 'disordered' region
Similar variants
- PRRC2C c.1055+2T>C Uncertain significance ★ same type
- PRRC2C p.Ala104Thr Uncertain significance ★ same type
- PRRC2C p.Ala1120Thr Uncertain significance ★ same type
- PRRC2C p.Ala1762Ser Uncertain significance ★ same type
- PRRC2C p.Ala1774Ser Uncertain significance ★ same type
- PRRC2C p.Ala1785Val Uncertain significance ★ same type
- PRRC2C p.Ala1927Thr Uncertain significance ★ same type
- PRRC2C p.Ala1930Val Uncertain significance ★ same type
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/prrc2c-p-pro118ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown