Is POLE p.Asp339Ala (c.1016A>C) pathogenic?

POLE p.Asp339Ala (c.1016A>C) is classified Uncertain significance in POLE (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-05). AlphaMissense: ambiguous (0.4891); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with POLE p.Asp339Ala (c.1016A>C)?

POLE p.Asp339Ala (c.1016A>C) is associated with hereditary neoplastic syndrome (ClinVar).

How common is POLE p.Asp339Ala (c.1016A>C) in the general population?

POLE p.Asp339Ala (c.1016A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about POLE p.Asp339Ala (c.1016A>C)?

AlphaMissense predicts ambiguous (score 0.4891) — an in-silico prediction, not a clinical call.

POLE p.Asp339Ala

c.1016A>C · rs1060500865 · VCV2562910

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4891 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.4891	ambiguous
REVEL	0.368	indeterminate
SaProt	LLR -9.65	tolerated
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>C here scores Δ0.57 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.9	GERP 1.7, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 23 kb · p 0.0025 · regional, not allelic
Overall
CADD	25.3	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.

Variant & gene context

Gene: POLE
Protein: p.Asp339Ala
Coding: c.1016A>C
MANE Select: NM_006231
dbSNP: rs1060500865
Type: single nucleotide variant
Location: chr12:132676098 (GRCh38)
Gene constraint: LOEUF 0.75 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 80.32 · 18 PDB

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.Asp339Tyr Uncertain significance ★★ ⚠ same residue
POLE p.Asp339Val Uncertain significance ★★ ⚠ same residue
POLE p.Asp339= Benign/Likely benign ★★ same residue
POLE p.Asp339Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
POLE p.Asp339Gly Uncertain significance ★ ⚠ 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

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-asp339ala (accessed [today's date]).

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