Is RECQL4 p.Ser677Phe (c.2030C>T) pathogenic?

RECQL4 p.Ser677Phe (c.2030C>T) is classified Uncertain significance in RECQL4 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-01). AlphaMissense: likely pathogenic (0.8395); No allele count reported in gnomAD v4.1 (AN 1,560,522); Associated with Baller-Gerold syndrome.

What condition is associated with RECQL4 p.Ser677Phe (c.2030C>T)?

RECQL4 p.Ser677Phe (c.2030C>T) is associated with Baller-Gerold syndrome (ClinVar).

How common is RECQL4 p.Ser677Phe (c.2030C>T) in the general population?

RECQL4 p.Ser677Phe (c.2030C>T) is no allele count reported in gnomAD v4.1 (AN 1,560,522) (gnomAD).

What do computational predictors say about RECQL4 p.Ser677Phe (c.2030C>T)?

AlphaMissense predicts likely pathogenic (score 0.8395) — an in-silico prediction, not a clinical call.

RECQL4 p.Ser677Phe

c.2030C>T · rs1340252869 · VCV2771472

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8395 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,560,522)

Missense predictors

2/2 damaging

AlphaMissense, SaProt

Conditions

Baller-Gerold syndrome

Computational evidence

Protein change
AlphaMissense	0.8395	likely pathogenic · top 6% in RECQL4
SaProt	LLR -12.90	damaging
⇒ AlphaMissense and SaProt both call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 1.39	unconstrained · MANE · 6,350 bp · p 1.8e-56 · regional, not allelic
Overall
CADD	23.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; SaProt is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,560,522). 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.Ser677Phe
Coding: c.2030C>T
MANE Select: NM_004260
dbSNP: rs1340252869
Type: single nucleotide variant
Location: chr8:144513956 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 677: a β-strand

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.Ser677Cys Uncertain significance ★★ same residue
RECQL4 p.Ser677= Benign/Likely benign ★★ 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-ser677phe (accessed [today's date]).

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