RECQL4 p.Pro149=
c.447C>G · rs377485079 · VCV1944390
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00171%, 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 -0.51 | GERP -2.5 |
| Overall | ||
| CADD | 1.169 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00171%
Admixed American · 1/58,370 alleles
Overall
0.000125%
2/1,596,640 alleles · very rare
exomes 2/1,444,320 · genomes 0/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00171% | 58,370 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,714 |
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.Pro149=
- Coding
- c.447C>G
- MANE Select
- NM_004260
- dbSNP
- rs377485079
- Type
- single nucleotide variant
- Location
- chr8:144516672 (GRCh38)
- Gene constraint
- LOEUF 1.519 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32 · 2 PDB
- Residue 149
- the 'disordered' region
Similar variants
- RECQL4 p.Pro149Ala Uncertain significance ★★ ⚠ same residue
- RECQL4 p.Pro149Arg Uncertain significance ★★ ⚠ same residue
- RECQL4 p.Pro149Leu Uncertain significance ★★ ⚠ same residue
- RECQL4 p.Pro149Ser Uncertain significance ★★ ⚠ same residue
- RECQL4 p.Pro149Thr 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
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-pro149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown