RECQL4 p.Pro875=
c.2625C>T · rs2130671101 · VCV1082964
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00187%, amr)
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 -2.5 | GERP -2.1 |
| Overall | ||
| CADD | 0.418 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00187%
Admixed American · 1/53,496 alleles
Overall
0.000127%
2/1,570,530 alleles · very rare
exomes 2/1,418,160 · genomes 0/152,370 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00187% | 53,496 |
| European (non-Finnish) | 8.63e-05% | 1,158,353 |
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.Pro875=
- Coding
- c.2625C>T
- MANE Select
- NM_004260
- dbSNP
- rs2130671101
- Type
- single nucleotide variant
- Location
- chr8:144512977 (GRCh38)
- Gene constraint
- LOEUF 1.519 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32 · 2 PDB
- Residue 875
- a UniProt-annotated variant site (in rts2); the 'disordered' region
Similar variants
- RECQL4 p.Pro875Leu Uncertain significance ★★ ⚠ same residue
- RECQL4 p.Pro875Ser 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
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-pro875 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown