Is CHRM3 p.Pro392fs (c.1173_1184delinsT) pathogenic?

CHRM3 p.Pro392fs (c.11731184delinsT) is classified Pathogenic in CHRM3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2011-11-11). No gnomAD frequency available for this variant; Associated with prune belly syndrome.

What condition is associated with CHRM3 p.Pro392fs (c.1173_1184delinsT)?

CHRM3 p.Pro392fs (c.1173_1184delinsT) is associated with prune belly syndrome (ClinVar).

How common is CHRM3 p.Pro392fs (c.1173_1184delinsT) in the general population?

CHRM3 p.Pro392fs (c.1173_1184delinsT) is no gnomAD frequency available for this variant (gnomAD).

CHRM3 p.Pro392fs

c.1173_1184delinsT · rs587776862 · VCV29626

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

prune belly 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 LoF-intolerant gene
NMD	escapes	premature termination codon in the last exon (7 of 7) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.14	GERP -4.2, phastCons 0.7

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: CHRM3
Protein: p.Pro392fs
Coding: c.1173_1184delinsT
MANE Select: NM_001375978
dbSNP: rs587776862
Type: Indel
Location: chr1:239908624 (GRCh38)
Gene constraint: LOEUF 0.42 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.30 · 5 PDB

Full CHRM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

CHRM3 p.Ala585Thr Uncertain significance ★★ ⚠ same condition
CHRM3 p.Ala589Asp Uncertain significance ★★ ⚠ same condition
CHRM3 p.Arg310His Uncertain significance ★★ ⚠ same condition
CHRM3 p.Arg44Gln Uncertain significance ★★ ⚠ same condition
CHRM3 p.Arg569Cys Uncertain significance ★★ ⚠ same condition
CHRM3 p.Arg584His Uncertain significance ★★ ⚠ same condition
CHRM3 p.Asn340del Uncertain significance ★★ same condition
CHRM3 p.Asn444Thr 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/chrm3-p-pro392fs (accessed [today's date]).

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