RECQL p.Ala2=
c.6G>A · rs369723830 · VCV1580296
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0176%, afr)
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 -2.2 | GERP -4.3 |
| Overall | ||
| CADD | 6.913 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0176%
African / African-American · 13/73,922 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00823%
Overall
0.00232%
37/1,593,038 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0176% | 5,686 |
| Middle Eastern | 0.0166% | 6,022 |
| East Asian | 0.00454% | 22,031 |
| Admixed American | 0.00177% | 56,500 |
| European (non-Finnish) | 0.00171% | 58,516 |
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.Ala2=
- Coding
- c.6G>A
- MANE Select
- NM_002907
- dbSNP
- rs369723830
- Type
- single nucleotide variant
- Location
- chr12:21499565 (GRCh38)
- Gene constraint
- LOEUF 1.235 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.55 · 7 PDB
Similar variants
- RECQL p.Ala2Thr Uncertain significance ★★ ⚠ same residue
- RECQL p.Ala2Val Uncertain significance ★★ ⚠ same residue
- RECQL p.Ala2Pro 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
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-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown