PRRC2C p.Val1022=
c.3066A>G · VCV3387928
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.49%, mid)
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 -1.7 | GERP -4.4 |
| Overall | ||
| CADD | 0.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.49%
Middle Eastern · 151/6,062 alleles
Filtering AF
2.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.04%
Overall
0.488%
7,868/1,613,724 alleles · low-frequency
exomes 7,202/1,461,442 · genomes 666/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.49% | 40 |
| Ashkenazi Jewishnot grpmax-eligible | 0.669% | 149 |
| Admixed American | 0.627% | 159 |
| Remaining individualsnot grpmax-eligible | 0.597% | 167 |
| European (non-Finnish) | 0.552% | 181 |
| African / African-American | 0.153% | 652 |
| South Asian | 0.102% | 979 |
| Finnishnot grpmax-eligible | 0.0797% | 1,255 |
| East Asian | 0.00223% | 44,866 |
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.Val1022=
- Coding
- c.3066A>G
- MANE Select
- NM_001387844
- Type
- single nucleotide variant
- Location
- chr1:171540532 (GRCh38)
- Gene constraint
- LOEUF 0.287 · pLI 1.00 (gnomAD)
- Residue 1022
- 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-val1022 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown