RECQL p.Thr331=
c.993G>A · rs764491255 · VCV514891
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00644%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.1 | GERP -3.7 |
| Overall | ||
| CADD | 5.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00644%
European (non-Finnish) · 76/1,179,310 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00482%
Overall
0.00515%
83/1,612,950 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00644% | 15,517 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,812 |
| Admixed American | 0.00334% | 29,973 |
| East Asian | 0.00223% | 44,866 |
| African / African-American | 0.00134% | 74,862 |
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
- RECQL
- Protein
- p.Thr331=
- Coding
- c.993G>A
- MANE Select
- NM_002907
- dbSNP
- rs764491255
- Type
- single nucleotide variant
- Location
- chr12:21475781 (GRCh38)
- Gene constraint
- LOEUF 1.235 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.55 · 7 PDB
- Residue 331
- the helicase c-terminal domain; an α-helix
Similar variants
- RECQL p.Thr331Met Uncertain significance ★★ ⚠ same residue
- RECQL p.Thr331Pro Uncertain significance ★ ⚠ same residue
- RECQL c.1098+1G>A Uncertain significance ★★ same type
- RECQL c.1216+3A>G Uncertain significance ★★ same type
- RECQL c.1217-3C>T Uncertain significance ★★ same type
- RECQL c.1355+1G>A Uncertain significance ★★ same type
- RECQL c.1356-12A>G Uncertain significance ★★ same type
- RECQL c.1667+5G>C 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/recql-p-thr331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown