Is RECQL4 p.Arg962= (c.2886G>A) pathogenic?

RECQL4 p.Arg962= (c.2886G>A) is classified Likely benign in RECQL4 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-31). Very rare (popmax 0.0011%, sas); Associated with Inborn genetic diseases.

What condition is associated with RECQL4 p.Arg962= (c.2886G>A)?

RECQL4 p.Arg962= (c.2886G>A) is associated with Inborn genetic diseases (ClinVar).

How common is RECQL4 p.Arg962= (c.2886G>A) in the general population?

RECQL4 p.Arg962= (c.2886G>A) is very rare (popmax 0.0011%, sas) (gnomAD).

RECQL4 p.Arg962=

c.2886G>A · VCV3787976

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.31	acceptor gain · deltas
Pangolin	Δ0.32	gain · loss 0.16 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 1	GERP 0.79, phastCons 1
Overall
CADD	13.24	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,090 alleles

Overall 6.2e-05% 1/1,612,498 alleles · very rare exomes 1/1,460,166 · genomes 0/152,332 · joint denominator

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.Arg962=
Coding: c.2886G>A
MANE Select: NM_004260
Type: single nucleotide variant
Location: chr8:144512561 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 962: a turn; a UniProt-annotated variant site (in rts2)

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.Arg962Lys Uncertain significance ★ ⚠ same residue
RECQL4 p.Arg962Ser 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
RECQL4 p.Ala122Ser Uncertain significance ★★ ⚠ same condition
RECQL4 p.Ala152Gly Uncertain significance ★★ ⚠ same condition
RECQL4 p.Ala152Thr 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-arg962 (accessed [today's date]).

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