Is RECQL4 p.Thr139= (c.417C>T) pathogenic?

RECQL4 p.Thr139= (c.417C>T) is classified Likely benign in RECQL4 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-02). Very rare (popmax 8.68e-05%, nfe); Associated with Baller-Gerold syndrome.

What condition is associated with RECQL4 p.Thr139= (c.417C>T)?

RECQL4 p.Thr139= (c.417C>T) is associated with Baller-Gerold syndrome (ClinVar).

How common is RECQL4 p.Thr139= (c.417C>T) in the general population?

RECQL4 p.Thr139= (c.417C>T) is very rare (popmax 8.68e-05%, nfe) (gnomAD).

RECQL4 p.Thr139=

c.417C>T · rs1554903649 · VCV459497

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.68e-05%, nfe)

Conditions

Baller-Gerold syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.21 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.1	GERP -2.5, phastCons 0.001
Overall
CADD	3.319	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.68e-05% European (non-Finnish) · 1/1,152,648 alleles

Overall 6.43e-05% 1/1,555,380 alleles · very rare exomes 1/1,403,062 · genomes 0/152,318 · joint denominator

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.Thr139=
Coding: c.417C>T
MANE Select: NM_004260
dbSNP: rs1554903649
Type: single nucleotide variant
Location: chr8:144516702 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 139: the 'disordered' region

Full RECQL4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Baller-Gerold syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RECQL4 p.Thr139Ala Uncertain significance ★ ⚠ same residue
RECQL4 p.Thr139Pro 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-thr139 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown