Is POLE p.Ser459Phe (c.1376C>T) pathogenic?

POLE p.Ser459Phe (c.1376C>T) is classified Pathogenic in POLE (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-22). AlphaMissense: likely pathogenic (0.9993); Absent from gnomAD v4.1.

How common is POLE p.Ser459Phe (c.1376C>T) in the general population?

POLE p.Ser459Phe (c.1376C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about POLE p.Ser459Phe (c.1376C>T)?

AlphaMissense predicts likely pathogenic (score 0.9993) — an in-silico prediction, not a clinical call.

POLE p.Ser459Phe

c.1376C>T · rs765702675 · VCV2836186

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9993 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9993	likely pathogenic ✓ concordant with ClinVar · top 1% in POLE
REVEL	0.418	indeterminate
SaProt	LLR -14.96	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 23 kb · p 0.0025 · regional, not allelic
Overall
CADD	29.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Cancer therapy — CIViC

Disease	Therapies	Level	Significance
Colorectal Cancer		B	Better Outcome

Variant & gene context

Gene: POLE
Protein: p.Ser459Phe
Coding: c.1376C>T
MANE Select: NM_006231
dbSNP: rs765702675
Type: single nucleotide variant
Location: chr12:132673261 (GRCh38)
Gene constraint: LOEUF 0.75 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 80.32 · 18 PDB
Residue 459: an α-helix; a UniProt-annotated variant site (found in a colorectal sample; somatic mutation)

Full POLE gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

POLE p.Ser459Cys Uncertain significance ★★ ⚠ same residue
POLE p.Ser459= Benign/Likely benign ★★ same residue
POLE p.Ser459Thr 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
POLE p.Leu424Val 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-ser459phe (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown