Is RECQL p.Gln633= (c.1899A>G) pathogenic?

RECQL p.Gln633= (c.1899A>G) is classified Benign in RECQL (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-04). Common (popmax 29.3%, eas) — too common for a highly-penetrant pathogenic allele.

RECQL p.Gln633=

Q: How common is RECQL p.Gln633= (c.1899A>G) in the general population?

RECQL p.Gln633= (c.1899A>G) is common (popmax 29.3%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1899A>G · rs17849408 · VCV506624

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 29.3%, eas) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.5	GERP -2.6
Overall
CADD	4.297	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 29.3% East Asian · 13,079/44,684 alleles

Filtering AF 28.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 28.7%

Overall 9.68% 155,841/1,610,128 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	29.3%	3
African / African-American	12.5%	8
Ashkenazi Jewishnot grpmax-eligible	12.3%	8
Remaining individualsnot grpmax-eligible	11.2%	9
Admixed American	11.2%	9
Middle Eastern	11%	9
Finnishnot grpmax-eligible	10.1%	10
South Asian	9.97%	10
European (non-Finnish)	8.49%	12
Amishnot grpmax-eligible	5.04%	20

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.Gln633=
Coding: c.1899A>G
MANE Select: NM_024854 · reported on NM_002907
dbSNP: rs17849408
Type: single nucleotide variant
Location: chr12:21470245 (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-gln633 (accessed [today's date]).

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