Is POLQ p.Arg798= (c.2392C>A) pathogenic?

POLQ p.Arg798= (c.2392C>A) is classified Likely benign in POLQ (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-01). Very rare (popmax 0.00134%, afr).

How common is POLQ p.Arg798= (c.2392C>A) in the general population?

POLQ p.Arg798= (c.2392C>A) is very rare (popmax 0.00134%, afr) (gnomAD).

POLQ p.Arg798=

c.2392C>A · rs753866746 · VCV1790574

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.28	acceptor loss, 45 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.3	GERP 0.66, phastCons 1
Overall
CADD	11.97	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,890 alleles

Overall 6.2e-05% 1/1,613,890 alleles · very rare exomes 0/1,461,836 · genomes 1/152,054 · 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: POLQ
Protein: p.Arg798=
Coding: c.2392C>A
MANE Select: NM_199420
dbSNP: rs753866746
Type: single nucleotide variant
Location: chr3:121493608 (GRCh38)
Structure: AlphaFold pLDDT 70.62 · 19 PDB

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

Similar variants

POLQ p.Arg798Gln Uncertain significance ★ ⚠ same residue
POLQ p.Arg798Trp 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-arg798 (accessed [today's date]).

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