Is MYBPC3 p.Pro110fs (c.329del) pathogenic?

MYBPC3 p.Pro110fs (c.329del) is classified Pathogenic in MYBPC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-30). No allele count reported in gnomAD v4.1 (AN 1,523,144); Associated with hypertrophic cardiomyopathy.

What condition is associated with MYBPC3 p.Pro110fs (c.329del)?

MYBPC3 p.Pro110fs (c.329del) is associated with hypertrophic cardiomyopathy (ClinVar).

How common is MYBPC3 p.Pro110fs (c.329del) in the general population?

MYBPC3 p.Pro110fs (c.329del) is no allele count reported in gnomAD v4.1 (AN 1,523,144) (gnomAD).

MYBPC3 p.Pro110fs

c.329del · rs2495783781 · VCV2780212

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,523,144)

Conditions

hypertrophic cardiomyopathy

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 3 of 35
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.08	GERP 0.88
Region caveats
Repeat context	tandem	G-rich low complexity · ambiguous alignment · confidence, not pathogenicity

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,523,144). 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: MYBPC3
Protein: p.Pro110fs
Coding: c.329del
MANE Select: NM_000256
dbSNP: rs2495783781
Type: Deletion
Location: chr11:47350579 (GRCh38)
Gene constraint: LOEUF 0.915 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.43 · 17 PDB
Residue 110: the 'disordered' region

Full MYBPC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypertrophic cardiomyopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MYBPC3 p.Pro110_Ala113del Uncertain significance ★ same residue
MYBPC3 p.Pro110_Ala111insSerPro Uncertain significance ★ same residue
MYBPC3 c.1227-39_1263del Likely pathogenic ★★ same condition
MYBPC3 c.1235_1236delTT Pathogenic ★★ same condition
MYBPC3 c.1404delG Pathogenic/Likely pathogenic ★★ same condition
MYBPC3 c.1792delG Pathogenic ★★ same condition
MYBPC3 c.1800delA Pathogenic ★★ same condition
MYBPC3 c.2149-2del 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/mybpc3-p-pro110fs (accessed [today's date]).

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