Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, sas)
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 -0.071 | GERP -3.8, phastCons 0.24 |
| Overall | ||
| CADD | 5.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
South Asian · 1,140/91,060 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.17%
Overall
0.277%
4,475/1,613,998 alleles · low-frequency
exomes 4,231/1,461,714 · genomes 244/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.25% | 80 |
| Middle Eastern | 0.429% | 233 |
| European (non-Finnish) | 0.26% | 384 |
| Remaining individualsnot grpmax-eligible | 0.245% | 408 |
| African / African-American | 0.0506% | 1,975 |
| Admixed American | 0.04% | 2,501 |
| Finnishnot grpmax-eligible | 0.0312% | 3,201 |
| East Asian | 0.00223% | 44,850 |
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.Pro234=
- Coding
- c.702C>G
- MANE Select
- NM_182649
- dbSNP
- rs17353
- Type
- single nucleotide variant
- Location
- chr20:5115453 (GRCh38)
- Gene constraint
- LOEUF 0.42 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 94.38 · 103 PDB
Similar variants
- PCNA p.Cys148Ser Likely pathogenic ★★ same type
- PCNA p.Ser228Ile Uncertain significance ★★ ⚠ same type
- PCNA p.Ala242= Benign/Likely 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-pro234 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown