Is CHD7 p.Pro1782fs (c.5345del) pathogenic?

CHD7 p.Pro1782fs (c.5345del) is classified Pathogenic in CHD7 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-03-28). No gnomAD frequency available for this variant; Associated with CHARGE syndrome.

What condition is associated with CHD7 p.Pro1782fs (c.5345del)?

CHD7 p.Pro1782fs (c.5345del) is associated with CHARGE syndrome (ClinVar).

How common is CHD7 p.Pro1782fs (c.5345del) in the general population?

CHD7 p.Pro1782fs (c.5345del) is no gnomAD frequency available for this variant (gnomAD).

CHD7 p.Pro1782fs

c.5345del · rs2150801705 · VCV1326581

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

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 25 of 38
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.94	GERP -1.6, 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.Pro1782fs
Coding: c.5345del
MANE Select: NM_017780
dbSNP: rs2150801705
Type: Deletion
Location: chr8:60849094 (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

Similar variants

CHD7 p.Pro1782Leu Uncertain significance ★★ ⚠ same residue
CHD7 c.8078del Likely pathogenic ★★ same condition
CHD7 p.Arg969fs Pathogenic ★★ same condition
CHD7 p.Asn96fs Pathogenic ★★ same condition
CHD7 p.Asp1090fs Pathogenic/Likely pathogenic ★★ same condition
CHD7 p.Asp2684fs Pathogenic ★★ same condition
CHD7 p.Gln2426fs Pathogenic ★★ same condition
CHD7 p.Glu2450fs 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-pro1782fs (accessed [today's date]).

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