POLE p.Ser828=
c.2484C>T · rs1060504053 · VCV413529
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 Δ0.32 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.8 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 13.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,970 alleles
Overall
6.2e-05%
1/1,613,994 alleles · very rare
exomes 1/1,461,668 · genomes 0/152,326 · joint denominator
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
- POLE
- Protein
- p.Ser828=
- Coding
- c.2484C>T
- MANE Select
- NM_006231
- dbSNP
- rs1060504053
- Type
- single nucleotide variant
- Location
- chr12:132664447 (GRCh38)
- Gene constraint
- LOEUF 0.75 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.32 · 18 PDB
- Residue 828
- a UniProt-annotated variant site (in imagei)
Similar variants
- POLE p.Ser828Pro Uncertain significance ★★ ⚠ same residue
- POLE p.Ser828Phe Uncertain significance ★ ⚠ same residue
- POLE p.Ser828Thr Uncertain significance ★ ⚠ same residue
- POLE p.Ser828Tyr Uncertain significance ★ ⚠ same residue
- POLE c.1686+32C>G Pathogenic/Likely pathogenic ★★ same type
- POLE c.3276-1G>C Likely pathogenic ★★ same type
- POLE c.5678+1G>T Pathogenic ★★ same type
- POLE p.Gln1763Ter Pathogenic/Likely pathogenic ★★ 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/pole-p-ser828 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown