POLQ p.Asp820=
c.2460C>T · rs138858790 · VCV1791628
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, 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 1.5 | GERP 0.4, phastCons 1 |
| Overall | ||
| CADD | 5.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,868 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000434%
7/1,613,614 alleles · ultra-rare
exomes 6/1,461,558 · genomes 1/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,478 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
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.Asp820=
- Coding
- c.2460C>T
- MANE Select
- NM_199420
- dbSNP
- rs138858790
- Type
- single nucleotide variant
- Location
- chr3:121493540 (GRCh38)
- Structure
- AlphaFold pLDDT 70.62 · 19 PDB
- Residue 820
- the 'disordered' region
Similar variants
- POLQ p.Asp820Glu 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-asp820 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown