Is RECQL4 p.Pro298Ser (c.892C>T) pathogenic?

RECQL4 p.Pro298Ser (c.892C>T) is classified Uncertain significance in RECQL4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-06-05). AlphaMissense: likely benign (0.0671); Ultra-rare (popmax 0.0214%, afr); Associated with Baller-Gerold syndrome.

What condition is associated with RECQL4 p.Pro298Ser (c.892C>T)?

RECQL4 p.Pro298Ser (c.892C>T) is associated with Baller-Gerold syndrome, Rothmund-Thomson syndrome type 2 (ClinVar).

How common is RECQL4 p.Pro298Ser (c.892C>T) in the general population?

RECQL4 p.Pro298Ser (c.892C>T) is ultra-rare (popmax 0.0214%, afr) (gnomAD).

What do computational predictors say about RECQL4 p.Pro298Ser (c.892C>T)?

AlphaMissense predicts likely benign (score 0.0671) — an in-silico prediction, not a clinical call.

RECQL4 p.Pro298Ser

c.892C>T · rs892796827 · VCV645149

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0671 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0214%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Conditions

Baller-Gerold syndrome

Computational evidence

Protein change
AlphaMissense	0.0671	likely benign
SaProt	LLR -5.82	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.82	GERP -3.3
Regional constraint	o/e 1.39	unconstrained · MANE · 6,350 bp · p 1.8e-56 · regional, not allelic
Overall
CADD	0.05	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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

Grpmax group 0.0214% African / African-American · 16/74,924 alleles

Filtering AF 0.0133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0109%

Overall 0.00186% 30/1,613,022 alleles · ultra-rare exomes 27/1,460,832 · genomes 3/152,190 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0214%	4,683
East Asian	0.00223%	44,894
Remaining individualsnot grpmax-eligible	0.0016%	62,444
European (non-Finnish)	0.00102%	98,320

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.Pro298Ser
Coding: c.892C>T
MANE Select: NM_004260
dbSNP: rs892796827
Type: single nucleotide variant
Location: chr8:144516227 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 298: 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

Also linked: Rothmund-Thomson syndrome type 2

Similar variants

RECQL4 p.Pro298Leu Uncertain significance ★★ ⚠ same residue
RECQL4 p.Pro298Thr 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-pro298ser (accessed [today's date]).

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