Is CHD7 p.Arg2568fs (c.7701_7702del) pathogenic?

CHD7 p.Arg2568fs (c.77017702del) is classified Pathogenic in CHD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-20). No gnomAD frequency available for this variant; Associated with CHARGE syndrome.

What condition is associated with CHD7 p.Arg2568fs (c.7701_7702del)?

CHD7 p.Arg2568fs (c.7701_7702del) is associated with CHARGE syndrome, hypogonadotropic hypogonadism 5 with or without anosmia (ClinVar).

How common is CHD7 p.Arg2568fs (c.7701_7702del) in the general population?

CHD7 p.Arg2568fs (c.7701_7702del) is no gnomAD frequency available for this variant (gnomAD).

CHD7 p.Arg2568fs

c.7701_7702del · rs1805943625 · VCV973215

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

CHARGE syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 35 of 38
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.9	GERP 2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHD7
Protein: p.Arg2568fs
Coding: c.7701_7702del
MANE Select: NM_017780
dbSNP: rs1805943625
Type: Microsatellite
Location: chr8:60860992 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

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

Also linked: hypogonadotropic hypogonadism 5 with or without anosmia

Similar variants

CHD7 p.Arg2568Trp Conflicting classifications of pathogenicity ★ same residue
CHD7 p.Arg2568Gln Likely benign ★ same residue
CHD7 p.Glu974_Gly975insTer Pathogenic ★★ same condition
CHD7 p.Phe2124del Pathogenic/Likely pathogenic ★★ same condition
CHD7 p.Thr64fs Pathogenic ★★ same condition
CHD7 p.Val1141fs Pathogenic ★★ same condition
CHD7 p.2760NLQ[1] Uncertain significance ★★ same condition
CHD7 p.2760NLQ[3] Uncertain significance ★★ 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-arg2568fs (accessed [today's date]).

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