POLQ p.Ala115=
c.345T>C · rs141638362 · VCV1731634
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.398%, nfe)
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 3.7 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 14.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.398%
European (non-Finnish) · 4,663/1,171,870 alleles
Filtering AF
0.388%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.384%
Overall
0.336%
5,336/1,588,306 alleles · rare
exomes 4,980/1,435,964 · genomes 356/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.398% | 251 |
| Remaining individualsnot grpmax-eligible | 0.358% | 279 |
| Finnishnot grpmax-eligible | 0.315% | 317 |
| Admixed American | 0.213% | 469 |
| South Asian | 0.104% | 960 |
| Middle Eastern | 0.0676% | 1,479 |
| African / African-American | 0.0627% | 1,595 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00707% | 14,142 |
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.Ala115=
- Coding
- c.345T>C
- MANE Select
- NM_199420
- dbSNP
- rs141638362
- Type
- single nucleotide variant
- Location
- chr3:121541478 (GRCh38)
- Structure
- AlphaFold pLDDT 70.62 · 19 PDB
- Residue 115
- the umuc domain; an α-helix
Similar variants
- POLQ p.Ala115Val 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
- POLQ p.Met1707Val 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-ala115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown