Is RECQL4 p.Ile703= (c.2109T>C) pathogenic?

RECQL4 p.Ile703= (c.2109T>C) is classified Likely benign in RECQL4 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-06-15). Very rare (popmax 0.00383%, amr); Associated with Inborn genetic diseases.

What condition is associated with RECQL4 p.Ile703= (c.2109T>C)?

RECQL4 p.Ile703= (c.2109T>C) is associated with Inborn genetic diseases, Baller-Gerold syndrome (ClinVar).

How common is RECQL4 p.Ile703= (c.2109T>C) in the general population?

RECQL4 p.Ile703= (c.2109T>C) is very rare (popmax 0.00383%, amr) (gnomAD).

RECQL4 p.Ile703=

c.2109T>C · rs759753484 · VCV705577

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00383%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -3.3, phastCons 1
Overall
CADD	10.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00383% Admixed American · 2/52,162 alleles

Filtering AF 0.00082% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000664%

Overall 0.00128% 20/1,562,956 alleles · very rare exomes 16/1,411,172 · genomes 4/151,784 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00383%	26,081
Remaining individualsnot grpmax-eligible	0.00165%	60,662
European (non-Finnish)	0.00139%	72,147
African / African-American	0.00136%	73,504

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.Ile703=
Coding: c.2109T>C
MANE Select: NM_004260
dbSNP: rs759753484
Type: single nucleotide variant
Location: chr8:144513662 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 703: the helicase c-terminal domain; a β-strand

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

Also linked: Baller-Gerold syndrome

Similar variants

RECQL4 p.Ile703Asn Uncertain significance ★ ⚠ same residue
RECQL4 p.Ile703Met Uncertain significance ★ ⚠ same residue
RECQL4 p.Ile703Val Conflicting classifications of pathogenicity ★ ⚠ same residue
RECQL4 c.1132-1G>A Likely pathogenic ★★ same condition
RECQL4 c.1259-1G>A Pathogenic/Likely pathogenic ★★ same condition
RECQL4 c.1391-1G>A Pathogenic ★★ same condition
RECQL4 c.1704+1G>A Pathogenic/Likely pathogenic ★★ same condition
RECQL4 c.1704+2T>G Likely pathogenic ★★ 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-ile703 (accessed [today's date]).

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