BIN1 (O00499) variants and mutations

BIN1 (also known as O00499) is a human protein-coding gene encoding a myc box-dependent-interacting protein 1 protein. It shapes cellular membranes and participates in endocytosis, T-tubule organization in muscle, and membrane trafficking in neurons. Pathogenic variants can cause centronuclear myopathy, while common variation at the BIN1 locus is strongly associated with late-onset Alzheimer disease risk. This analysis covers 836 BIN1 variants and mutations. Of these, 80% have computational variant effect predictions. Disease context includes myopathy, centronuclear, 2, autosomal recessive centronuclear myopathy, and Alzheimer disease. Example BIN1 variants include A2V, E3D, and M4I.

Variant analysis overview

Gene: BIN1
Protein: O00499
UniProt accession: O00499
Organism: Homo sapiens
Variants analyzed: 836
Variant scope: all variants
Completed: 2026-08-21

Variant and mutation evidence

Variant composition: 667 unspecified-consequence records; 1 stop retained variant; 85 missense variants; 67 synonymous variants; 6 frameshift variants; 4 stop-gained variants; 2 in-frame deletions; 4 splice-region variants; 1 in-frame insertions; 2 substitution
Prediction scores: 669 variants have prediction scores (80% of the analyzed set).

Clinical, disease, and population context

Disease context: 25 disease associations are represented. Top associations: myopathy, centronuclear, 2, autosomal recessive centronuclear myopathy, Alzheimer disease, autosomal dominant centronuclear myopathy, centronuclear myopathy, dementia, neurodegenerative disease, Abnormality of the skeletal system, Lewy body dementia, memory impairment, late-onset Alzheimers disease, hypertensive disorder.

Protein structure and variant hotspots

Protein features: 2 domains; 7 post-translational modification sites.
Structural context: 409 variants have structural context.
PTM context: 12 variants overlap post-translational modification sites.

Data sources

Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.

Notable BIN1 variants

Examples include A2V, E3D, M4I, M4T, M4V, G5D, G5E, K7R. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.

BIN1 analysis run — BIN1 (836 variants) — completed 2026-08-21