Is POLQ p.Asp487= (c.1461C>T) pathogenic?

POLQ p.Asp487= (c.1461C>T) is classified Likely benign in POLQ (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-27). No allele count reported in gnomAD v4.1 (AN 1,529,180).

How common is POLQ p.Asp487= (c.1461C>T) in the general population?

POLQ p.Asp487= (c.1461C>T) is no allele count reported in gnomAD v4.1 (AN 1,529,180) (gnomAD).

POLQ p.Asp487=

c.1461C>T · rs2546809971 · VCV2625847

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,529,180)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.36	GERP -0.34, phastCons 0.98
Overall
CADD	3.359	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,529,180). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: POLQ
Protein: p.Asp487=
Coding: c.1461C>T
MANE Select: NM_199420
dbSNP: rs2546809971
Type: single nucleotide variant
Location: chr3:121519878 (GRCh38)
Structure: AlphaFold pLDDT 70.62 · 19 PDB
Residue 487: an α-helix

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

Similar variants

POLK p.Ile487Thr Pathogenic ★ ⚠ same residue
POLQ p.Asp487Gly Uncertain significance ★ ⚠ same residue
POLQ p.Arg2169Cys Uncertain significance ★★ ⚠ same type
POLQ p.Arg2347Cys Uncertain significance ★★ ⚠ same type
POLQ p.Cys2219Tyr Uncertain significance ★★ ⚠ same type
POLQ p.Glu2246Lys Uncertain significance ★★ ⚠ same type
POLQ p.Glu731Ala Uncertain significance ★★ ⚠ same type
POLQ p.Lys68Glu Uncertain significance ★★ ⚠ 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/polq-p-asp487 (accessed [today's date]).

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