Is POLE p.Ser1931Phe (c.5792C>T) pathogenic?

POLE p.Ser1931Phe (c.5792C>T) is classified Conflicting classifications of pathogenicity in POLE (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-10-23). AlphaMissense: likely benign (0.1635); Very rare (popmax 8.48e-05%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with POLE p.Ser1931Phe (c.5792C>T)?

POLE p.Ser1931Phe (c.5792C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is POLE p.Ser1931Phe (c.5792C>T) in the general population?

POLE p.Ser1931Phe (c.5792C>T) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about POLE p.Ser1931Phe (c.5792C>T)?

AlphaMissense predicts likely benign (score 0.1635) — an in-silico prediction, not a clinical call.

POLE p.Ser1931Phe

c.5792C>T · rs879254232 · VCV246386

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1635 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1635	likely benign
REVEL	0.18	moderately benign-leaning
SaProt	LLR -9.87	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4.4	phastCons 0.91
Regional constraint	o/e 0.92	unconstrained · MANE · 36 kb · p 0.001 · regional, not allelic
Overall
CADD	21.8	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

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,810 alleles

Overall 6.2e-05% 1/1,613,696 alleles · very rare exomes 1/1,461,354 · genomes 0/152,342 · 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.Ser1931Phe
Coding: c.5792C>T
MANE Select: NM_006231
dbSNP: rs879254232
Type: single nucleotide variant
Location: chr12:132635911 (GRCh38)
Gene constraint: LOEUF 0.75 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 80.32 · 18 PDB
Residue 1931: a UniProt-annotated variant site (in imagei)

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

POLE p.Ser1931Ala Uncertain significance ★ ⚠ same residue
POLE p.Ser1931Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
POLE p.Ser1931Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
POLE p.Ser1931= Likely benign ★ same residue
POLE c.1686+32C>G Pathogenic/Likely pathogenic ★★ same condition
POLE p.Leu424Val Pathogenic ★★ same condition
POLE c.1020+5G>A Uncertain significance ★★ same condition
POLE c.1106+3G>C Uncertain significance ★★ same condition

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-ser1931phe (accessed [today's date]).

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