Is RECQL4 p.Arg709= (c.2127G>A) pathogenic?

RECQL4 p.Arg709= (c.2127G>A) is classified Likely benign in RECQL4 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-04). No allele count reported in gnomAD v4.1 (AN 1,583,868); Associated with Inborn genetic diseases.

What condition is associated with RECQL4 p.Arg709= (c.2127G>A)?

RECQL4 p.Arg709= (c.2127G>A) is associated with Inborn genetic diseases (ClinVar).

How common is RECQL4 p.Arg709= (c.2127G>A) in the general population?

RECQL4 p.Arg709= (c.2127G>A) is no allele count reported in gnomAD v4.1 (AN 1,583,868) (gnomAD).

RECQL4 p.Arg709=

c.2127G>A · VCV4863159

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,583,868)

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 -3.4	GERP -3.9
Overall
CADD	1.286	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,583,868). 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.Arg709=
Coding: c.2127G>A
MANE Select: NM_004260
Type: single nucleotide variant
Location: chr8:144513644 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 709: the helicase c-terminal domain; a β-strand

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

Similar variants

RECQL4 p.Arg709Gly Uncertain significance ★★ same residue
RECQL4 p.Arg709Trp Uncertain significance ★★ ⚠ same residue
RECQL4 p.Arg709Leu Uncertain significance ★ same residue
RECQL4 p.Arg709Pro Uncertain significance ★ ⚠ same residue
RECQL4 p.Arg709Gln Uncertain significance ★ ⚠ same residue
RECQL4 p.Ala1001Thr Uncertain significance ★★ ⚠ same condition
RECQL4 p.Ala1066Thr Uncertain significance ★★ ⚠ same condition
RECQL4 p.Ala1174Pro Uncertain significance ★★ ⚠ 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-arg709 (accessed [today's date]).

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