RECQL4 p.Pro169=
c.507A>G · rs755588645 · VCV414178
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0172%, nfe)
Conditions
2
Inborn genetic diseases
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 -0.42 | GERP -2.7, phastCons 0.037 |
| Overall | ||
| CADD | 4.353 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0172%
European (non-Finnish) · 203/1,178,990 alleles
Filtering AF
0.0152%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0145%
Overall
0.0135%
218/1,610,702 alleles · ultra-rare
exomes 211/1,458,484 · genomes 7/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0172% | 5,808 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,794 |
| South Asian | 0.0044% | 22,724 |
| African / African-American | 0.00401% | 24,957 |
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
- RECQL4
- Protein
- p.Pro169=
- Coding
- c.507A>G
- MANE Select
- NM_004260
- dbSNP
- rs755588645
- Type
- single nucleotide variant
- Location
- chr8:144516612 (GRCh38)
- Gene constraint
- LOEUF 1.519 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32 · 2 PDB
- Residue 169
- the 'disordered' region
Similar variants
- RECQL4 p.Pro169Leu Uncertain significance ★ ⚠ same residue
- RECQL4 c.1132-1G>A Likely pathogenic ★★ same condition
- RECQL4 c.1259-1G>A Pathogenic/Likely pathogenic ★★ same condition
- RECQL4 c.1391-1G>A Pathogenic ★★ same condition
- RECQL4 c.1704+1G>A Pathogenic/Likely pathogenic ★★ same condition
- RECQL4 c.1704+2T>G Likely pathogenic ★★ same condition
- RECQL4 c.1705-1G>A Likely pathogenic ★★ same condition
- RECQL4 c.1705-1G>C Likely pathogenic ★★ same condition
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/recql4-p-pro169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown