PCNA p.Ala242=
c.726G>A · rs147737215 · VCV711223
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.343%, afr)
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 0.65 | GERP -1.9, phastCons 0.9 |
| Overall | ||
| CADD | 12.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.343%
African / African-American · 257/75,004 alleles
Filtering AF
0.308%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.295%
Overall
0.0437%
706/1,613,786 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.343% | 292 |
| Middle Eastern | 0.33% | 303 |
| South Asian | 0.104% | 959 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,838 |
| Admixed American | 0.0267% | 3,751 |
| European (non-Finnish) | 0.0236% | 4,229 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,798 |
| Finnishnot grpmax-eligible | 0.00469% | 21,340 |
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
- PCNA
- Protein
- p.Ala242=
- Coding
- c.726G>A
- MANE Select
- NM_182649
- dbSNP
- rs147737215
- Type
- single nucleotide variant
- Location
- chr20:5115343 (GRCh38)
- Gene constraint
- LOEUF 0.42 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 94.38 · 103 PDB
- Residue 242
- a turn
Similar variants
- PCNA p.Cys148Ser Likely pathogenic ★★ same type
- PCNA p.Ser228Ile Uncertain significance ★★ ⚠ same type
- PCNA p.Pro234= Benign ★★ same type
- PCNA p.Arg53Gln Uncertain significance ★ ⚠ same type
- PCNA p.Asn24Ser Uncertain significance ★ ⚠ same type
- PCNA p.Gly56Ser Uncertain significance ★ ⚠ same type
- PCNA p.Leu182Phe Uncertain significance ★ ⚠ same type
- PCNA p.Leu182Trp 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/pcna-p-ala242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown