Is CHD7 p.Arg1069Pro (c.3206G>C) pathogenic?

CHD7 p.Arg1069Pro (c.3206G>C) is classified Uncertain significance in CHD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-16). AlphaMissense: likely pathogenic (0.8763); Absent from gnomAD v4.1; Associated with CHARGE syndrome.

What condition is associated with CHD7 p.Arg1069Pro (c.3206G>C)?

CHD7 p.Arg1069Pro (c.3206G>C) is associated with CHARGE syndrome (ClinVar).

How common is CHD7 p.Arg1069Pro (c.3206G>C) in the general population?

CHD7 p.Arg1069Pro (c.3206G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHD7 p.Arg1069Pro (c.3206G>C)?

AlphaMissense predicts likely pathogenic (score 0.8763) — an in-silico prediction, not a clinical call.

CHD7 p.Arg1069Pro

c.3206G>C · rs1346050533 · VCV2172366

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8763 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

CHARGE syndrome

Computational evidence

Protein change
AlphaMissense	0.8763	likely pathogenic
REVEL	0.668	pathogenic-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this damaging; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 0.55	unconstrained · MANE · 14 kb · p 1.9e-20 · regional, not allelic
Overall
CADD	25.5	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 is an independent agreement signal.

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.Arg1069Pro
Coding: c.3206G>C
MANE Select: NM_017780
dbSNP: rs1346050533
Type: single nucleotide variant
Location: chr8:60823844 (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.Arg1069= Likely benign ★ 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-arg1069pro (accessed [today's date]).

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