Is RECQL4 p.Arg96= (c.286C>A) pathogenic?

RECQL4 p.Arg96= (c.286C>A) is classified Likely benign in RECQL4 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-19). Rare (popmax 0.14%, afr); Associated with Inborn genetic diseases.

What condition is associated with RECQL4 p.Arg96= (c.286C>A)?

RECQL4 p.Arg96= (c.286C>A) is associated with Inborn genetic diseases, Baller-Gerold syndrome, hereditary neoplastic syndrome (ClinVar).

How common is RECQL4 p.Arg96= (c.286C>A) in the general population?

RECQL4 p.Arg96= (c.286C>A) is rare (popmax 0.14%, afr) (gnomAD).

RECQL4 p.Arg96=

c.286C>A · rs375568877 · VCV239749

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.14%, afr)

Conditions

Inborn genetic diseases

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 1.4	GERP 0.36, phastCons 0.001
Overall
CADD	4.538	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.14% African / African-American · 105/75,064 alleles

Filtering AF 0.118% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.11%

Overall 0.00788% 127/1,612,298 alleles · rare exomes 65/1,459,938 · genomes 62/152,360 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.14%	715
Middle Eastern	0.0165%	6,052
Remaining individualsnot grpmax-eligible	0.0032%	31,220
Admixed American	0.00167%	59,994
European (non-Finnish)	0.00153%	65,540

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.Arg96=
Coding: c.286C>A
MANE Select: NM_004260
dbSNP: rs375568877
Type: single nucleotide variant
Location: chr8:144517118 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 96: the 'disordered' region

Full RECQL4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Baller-Gerold syndrome hereditary neoplastic syndrome

Similar variants

RECQL4 p.Arg96Gln Uncertain significance ★★ ⚠ same residue
RECQL4 p.Arg96Trp 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-arg96 (accessed [today's date]).

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