Is RECQL p.Ala459Pro (c.1375G>C) pathogenic?

RECQL p.Ala459Pro (c.1375G>C) is classified Uncertain significance in RECQL (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-03). AlphaMissense: likely pathogenic (0.9907); Absent from gnomAD v4.1.

How common is RECQL p.Ala459Pro (c.1375G>C) in the general population?

RECQL p.Ala459Pro (c.1375G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about RECQL p.Ala459Pro (c.1375G>C)?

AlphaMissense predicts likely pathogenic (score 0.9907) — an in-silico prediction, not a clinical call.

RECQL p.Ala459Pro

c.1375G>C · rs1055710310 · VCV1771145

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9907 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.9907	likely pathogenic · top 5% in RECQL
REVEL	0.401	indeterminate
SaProt	LLR -16.82	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.3	GERP 2, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 29 kb · p 0.095 · regional, not allelic
Overall
CADD	29.7	PHRED · no single calibrated threshold — expert panels disagree

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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: RECQL
Protein: p.Ala459Pro
Coding: c.1375G>C
MANE Select: NM_002907
dbSNP: rs1055710310
Type: single nucleotide variant
Location: chr12:21473623 (GRCh38)
Gene constraint: LOEUF 1.235 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.55 · 7 PDB
Residue 459: a UniProt-annotated variant site (in recon; likely pathogenic; reduces dna helicase activity on a forked duplex dna substrate; decreases atpase activity; reduces dna-binding; defect in repairing abortive top1/topoisomerase 1 and top2/topoisomerase 2 cleavage complexes; failure to efficiently restart replication following exposure to genotoxins, such as hydroxyurea (hu) and methyl methane sulfonate (mms); no impact on nuclear localization and interaction with parp1; no effect on capacity to promote single-strand dna annealing); an α-helix

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

Similar variants

RECQL p.Ala459Ser Uncertain significance ★★ ⚠ same residue
RECQL p.Ala459Thr Uncertain significance ★ ⚠ same residue
RECQL p.Ala459= Likely benign ★ same residue
RECQL c.1098+1G>A Uncertain significance ★★ same type
RECQL c.1216+3A>G Uncertain significance ★★ same type
RECQL c.1217-3C>T Uncertain significance ★★ same type
RECQL c.1355+1G>A Uncertain significance ★★ same type
RECQL c.1356-12A>G Uncertain significance ★★ same type

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-ala459pro (accessed [today's date]).

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