Is RECQL4 p.Phe404fs (c.1211del) pathogenic?

RECQL4 p.Phe404fs (c.1211del) is classified Pathogenic in RECQL4 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-30). No gnomAD frequency available for this variant; Associated with Baller-Gerold syndrome.

What condition is associated with RECQL4 p.Phe404fs (c.1211del)?

RECQL4 p.Phe404fs (c.1211del) is associated with Baller-Gerold syndrome (ClinVar).

How common is RECQL4 p.Phe404fs (c.1211del) in the general population?

RECQL4 p.Phe404fs (c.1211del) is no gnomAD frequency available for this variant (gnomAD).

RECQL4 p.Phe404fs

c.1211del · rs2130712718 · VCV1456965

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Baller-Gerold syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 6 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.3	GERP -3.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: RECQL4
Protein: p.Phe404fs
Coding: c.1211del
MANE Select: NM_004260
dbSNP: rs2130712718
Type: Deletion
Location: chr8:144515811 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB

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.Phe404Leu Uncertain significance ★ same residue
RECQL4 p.Phe404Ser Uncertain significance ★ same residue
RECQL4 p.Phe404= Likely benign ★ same residue
RECQL4 c.1131_1131+3del Pathogenic/Likely pathogenic ★★ same condition
RECQL4 c.1390+2del Pathogenic ★★ same condition
RECQL4 c.359_374delGACCAGCCCTGGGCCG Pathogenic/Likely pathogenic ★★ same condition
RECQL4 p.Ala1045fs Pathogenic ★★ same condition
RECQL4 p.Ala291fs 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-phe404fs (accessed [today's date]).

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