Is RECQL4 p.Leu1007= (c.3021C>T) pathogenic?

RECQL4 p.Leu1007= (c.3021C>T) is classified Likely benign in RECQL4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-15). Very rare (popmax 0.00835%, amr); Associated with Baller-Gerold syndrome.

What condition is associated with RECQL4 p.Leu1007= (c.3021C>T)?

RECQL4 p.Leu1007= (c.3021C>T) is associated with Baller-Gerold syndrome (ClinVar).

How common is RECQL4 p.Leu1007= (c.3021C>T) in the general population?

RECQL4 p.Leu1007= (c.3021C>T) is very rare (popmax 0.00835%, amr) (gnomAD).

RECQL4 p.Leu1007=

c.3021C>T · rs1301549552 · VCV719638

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00835%, amr)

Conditions

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 -0.35	GERP -3.9
Overall
CADD	0.605	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00835% Admixed American · 5/59,880 alleles

Filtering AF 0.00324% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.000746% 12/1,608,570 alleles · very rare exomes 10/1,456,316 · genomes 2/152,254 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00835%	11,976
South Asian	0.0011%	90,982
European (non-Finnish)	0.00051%	196,208

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.Leu1007=
Coding: c.3021C>T
MANE Select: NM_004260
dbSNP: rs1301549552
Type: single nucleotide variant
Location: chr8:144512426 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 1007: an α-helix; a UniProt-annotated variant site (in rts2)

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.Leu1007Phe Uncertain significance ★★ ⚠ same residue
RECQL4 p.Leu1007Ile 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-leu1007 (accessed [today's date]).

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