RECQL4 p.Ser555=
c.1665G>A · rs756736123 · VCV1027263
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00891%, eas)
Conditions
1
Baller-Gerold syndrome
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 -12 | GERP -3.6 |
| Overall | ||
| CADD | 0.092 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,872 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.00229%
37/1,612,304 alleles · very rare
exomes 33/1,460,018 · genomes 4/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,218 |
| African / African-American | 0.00267% | 37,519 |
| European (non-Finnish) | 0.00263% | 38,052 |
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.Ser555=
- Coding
- c.1665G>A
- MANE Select
- NM_004260
- dbSNP
- rs756736123
- Type
- single nucleotide variant
- Location
- chr8:144514481 (GRCh38)
- Gene constraint
- LOEUF 1.519 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32 · 2 PDB
- Residue 555
- the helicase atp-binding domain
Similar variants
- RECQL4 p.Ser555Trp Uncertain significance ★★ same residue
- RECQL4 p.Ser555Leu 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-ser555 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown