POLQ p.Ala258=
c.774T>C · VCV3308637
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -5.5 | GERP -2.2 |
| Overall | ||
| CADD | 1.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,820 alleles
Overall
0.000124%
2/1,609,460 alleles · very rare
exomes 2/1,457,086 · genomes 0/152,374 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,820 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,310 |
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.Ala258=
- Coding
- c.774T>C
- MANE Select
- NM_199420
- Type
- single nucleotide variant
- Location
- chr3:121533176 (GRCh38)
- Structure
- AlphaFold pLDDT 70.62 · 19 PDB
- Residue 258
- the umuc domain
Similar variants
- 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
- POLQ p.Met1707Val Uncertain significance ★★ ⚠ same type
- POLQ p.Thr1010Ala 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-ala258 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown