Is POLE p.Asp1663Val (c.4988A>T) pathogenic?

POLE p.Asp1663Val (c.4988A>T) is classified Uncertain significance in POLE (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-02-18). AlphaMissense: likely pathogenic (0.6294); Very rare (popmax 6.99e-05%); Associated with hereditary neoplastic syndrome.

What condition is associated with POLE p.Asp1663Val (c.4988A>T)?

POLE p.Asp1663Val (c.4988A>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is POLE p.Asp1663Val (c.4988A>T) in the general population?

POLE p.Asp1663Val (c.4988A>T) is very rare (popmax 6.99e-05%) (gnomAD).

What do computational predictors say about POLE p.Asp1663Val (c.4988A>T)?

AlphaMissense predicts likely pathogenic (score 0.6294) — an in-silico prediction, not a clinical call.

POLE p.Asp1663Val

c.4988A>T · rs2042165436 · VCV1058896

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.6294 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 6.99e-05%)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.6294	likely pathogenic
REVEL	0.843	moderately pathogenic-leaning
SaProt	LLR -6.03	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 36 kb · p 0.001 · regional, not allelic
Overall
CADD	28.9	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 6.99e-05%

Overall 6.99e-05% 1/1,430,912 alleles · very rare

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.Asp1663Val
Coding: c.4988A>T
MANE Select: NM_006231
dbSNP: rs2042165436
Type: single nucleotide variant
Location: chr12:132642362 (GRCh38)
Gene constraint: LOEUF 0.75 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 80.32 · 18 PDB
Residue 1663: a turn; 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.Asp1663Asn Uncertain significance ★★ ⚠ same residue
POLE p.Asp1663His Uncertain significance ★★ ⚠ same residue
POLE p.Asp1663= 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
POLE c.1106+4A>G 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-asp1663val (accessed [today's date]).

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