Is RECQL p.Asp648= (c.1944T>C) pathogenic?

RECQL p.Asp648= (c.1944T>C) is classified Likely benign in RECQL (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-19). Ultra-rare (popmax 0.0112%, eas).

How common is RECQL p.Asp648= (c.1944T>C) in the general population?

RECQL p.Asp648= (c.1944T>C) is ultra-rare (popmax 0.0112%, eas) (gnomAD).

RECQL p.Asp648=

c.1944T>C · rs775565257 · VCV1783108

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0112%, eas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 0.55	GERP 0.4, phastCons 0.037
Overall
CADD	6.087	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0112% East Asian · 5/44,788 alleles

Filtering AF 0.00435% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00276%

Overall 0.00031% 5/1,611,706 alleles · ultra-rare exomes 5/1,459,722 · genomes 0/151,984 · 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: RECQL
Protein: p.Asp648=
Coding: c.1944T>C
MANE Select: NM_002907
dbSNP: rs775565257
Type: single nucleotide variant
Location: chr12:21470200 (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-asp648 (accessed [today's date]).

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