Is RECQL p.Lys613Arg (c.1838A>G) pathogenic?

RECQL p.Lys613Arg (c.1838A>G) is classified Uncertain significance in RECQL (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-12-25). AlphaMissense: likely benign (0.0653); Very rare (popmax 0.000595%, nfe).

How common is RECQL p.Lys613Arg (c.1838A>G) in the general population?

RECQL p.Lys613Arg (c.1838A>G) is very rare (popmax 0.000595%, nfe) (gnomAD).

What do computational predictors say about RECQL p.Lys613Arg (c.1838A>G)?

AlphaMissense predicts likely benign (score 0.0653) — an in-silico prediction, not a clinical call.

RECQL p.Lys613Arg

c.1838A>G · rs763815034 · VCV1781074

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0653 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000595%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0653	likely benign
REVEL	0.025	moderately benign-leaning
SaProt	LLR -6.71	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.65	GERP -3.2
Regional constraint	o/e 0.51	unconstrained · MANE · 772 bp · p 0.00019 · regional, not allelic
Overall
CADD	2.778	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; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000595% European (non-Finnish) · 7/1,175,982 alleles

Filtering AF 0.000248% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000481% 7/1,455,340 alleles · very rare

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: RECQL
Protein: p.Lys613Arg
Coding: c.1838A>G
MANE Select: NM_024854 · reported on NM_002907
dbSNP: rs763815034
Type: single nucleotide variant
Location: chr12:21470306 (GRCh38)

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

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/recql-p-lys613arg (accessed [today's date]).

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