Is CHD7 p.Arg1069= (c.3207A>G) pathogenic?

CHD7 p.Arg1069= (c.3207A>G) is classified Likely benign in CHD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-30). Absent from gnomAD v4.1; Associated with CHARGE syndrome.

What condition is associated with CHD7 p.Arg1069= (c.3207A>G)?

CHD7 p.Arg1069= (c.3207A>G) is associated with CHARGE syndrome (ClinVar).

How common is CHD7 p.Arg1069= (c.3207A>G) in the general population?

CHD7 p.Arg1069= (c.3207A>G) is absent from gnomAD v4.1 (gnomAD).

CHD7 p.Arg1069=

c.3207A>G · VCV3693251

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CHARGE syndrome

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 0.96	GERP -0.37, phastCons 0.98
Overall
CADD	8.561	PHRED · no single calibrated threshold — expert panels disagree

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: CHD7
Protein: p.Arg1069=
Coding: c.3207A>G
MANE Select: NM_017780
Type: single nucleotide variant
Location: chr8:60823845 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1069: the helicase atp-binding domain

Full CHD7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CHARGE syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHD7 p.Arg1069Ter Pathogenic ★★ same residue
CHD7 p.Arg1069Pro Uncertain significance ★ ⚠ same residue
CHD7 p.Arg1069Gln Likely benign ★ same residue
CHD7 p.Arg1069Gly Uncertain significance ★ same residue
CHD7 c.2097-2A>G Pathogenic ★★ same condition
CHD7 c.2238+1G>A Pathogenic ★★ same condition
CHD7 c.2377-1G>A Likely pathogenic ★★ same condition
CHD7 c.2613+1G>A Pathogenic/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/chd7-p-arg1069 (accessed [today's date]).

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