Is RECQL4 p.Ala960= (c.2880C>G) pathogenic?

RECQL4 p.Ala960= (c.2880C>G) is classified Conflicting classifications of pathogenicity in RECQL4 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-12-15). Absent from gnomAD v4.1; Associated with Baller-Gerold syndrome.

What condition is associated with RECQL4 p.Ala960= (c.2880C>G)?

RECQL4 p.Ala960= (c.2880C>G) is associated with Baller-Gerold syndrome (ClinVar).

How common is RECQL4 p.Ala960= (c.2880C>G) in the general population?

RECQL4 p.Ala960= (c.2880C>G) is absent from gnomAD v4.1 (gnomAD).

RECQL4 p.Ala960=

c.2880C>G · rs766684128 · VCV1029807

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

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	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.8	GERP -1.9, phastCons 1
Overall
CADD	14.88	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: RECQL4
Protein: p.Ala960=
Coding: c.2880C>G
MANE Select: NM_004260
dbSNP: rs766684128
Type: single nucleotide variant
Location: chr8:144512647 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 960: a turn; 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.Ala960Gly Uncertain significance ★ ⚠ same residue
RECQL4 p.Ala960Ser Uncertain significance ★ ⚠ same residue
RECQL4 p.Ala960Val Uncertain significance ★ ⚠ same residue
RECQL4 p.Ala960Thr 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

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-ala960 (accessed [today's date]).

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