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Aliases for BIN1 Gene

Aliases for BIN1 Gene

  • Bridging Integrator 1 2 3 4 5
  • Amphiphysin II 2 3 4
  • Box-Dependent Myc-Interacting Protein 1 3 4
  • Amphiphysin-Like Protein 3 4
  • AMPHL 3 4
  • Box Dependant MYC Interacting Protein 1 3
  • Myc Box-Dependent-Interacting Protein 1 3
  • AMPH2 3
  • SH3P9 3
  • CNM2 3

External Ids for BIN1 Gene

Previous HGNC Symbols for BIN1 Gene


Previous GeneCards Identifiers for BIN1 Gene

  • GC02M125104
  • GC02M125732
  • GC02M127710
  • GC02M127898
  • GC02M127521
  • GC02M120113
  • GC02M127805

Summaries for BIN1 Gene

Entrez Gene Summary for BIN1 Gene

  • This gene encodes several isoforms of a nucleocytoplasmic adaptor protein, one of which was initially identified as a MYC-interacting protein with features of a tumor suppressor. Isoforms that are expressed in the central nervous system may be involved in synaptic vesicle endocytosis and may interact with dynamin, synaptojanin, endophilin, and clathrin. Isoforms that are expressed in muscle and ubiquitously expressed isoforms localize to the cytoplasm and nucleus and activate a caspase-independent apoptotic process. Studies in mouse suggest that this gene plays an important role in cardiac muscle development. Alternate splicing of the gene results in several transcript variants encoding different isoforms. Aberrant splice variants expressed in tumor cell lines have also been described. [provided by RefSeq, Mar 2016]

GeneCards Summary for BIN1 Gene

BIN1 (Bridging Integrator 1) is a Protein Coding gene. Diseases associated with BIN1 include Myopathy, Centronuclear, 2 and Myopathy, Centronuclear, 1. Among its related pathways are Vesicle-mediated transport and Endocytosis. Gene Ontology (GO) annotations related to this gene include identical protein binding and protein complex binding. An important paralog of this gene is AMPH.

UniProtKB/Swiss-Prot for BIN1 Gene

  • May be involved in regulation of synaptic vesicle endocytosis. May act as a tumor suppressor and inhibits malignant cell transformation.

Gene Wiki entry for BIN1 Gene

Additional gene information for BIN1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BIN1 Gene

Genomics for BIN1 Gene

GeneHancer (GH) Regulatory Elements for BIN1 Gene

Promoters and enhancers for BIN1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I127099 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 566.4 +3.2 3159 8.6 ELF3 NFIB SIN3A ZNF48 RARA ZNF335 GLIS2 EGR1 EGR2 SP3 BIN1 LOC105373605 ENSG00000260634
GH02I127128 Enhancer 1.1 Ensembl ENCODE dbSUPER 24.8 -21.4 -21428 1.1 USF1 RXRA IRF5 MAX USF2 EBF1 RAD21 RFX5 YY1 ZNF335 BIN1 LOC105373605 NIFKP9
GH02I127071 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 16.4 +22.1 22089 28.4 HDGF PKNOX1 TCF12 GLIS2 ATF7 FOS RUNX3 ZNF623 ZNF592 ATF4 BIN1 GPR17 ENSG00000260634 MAP3K2
GH02I127024 Promoter/Enhancer 1.3 Ensembl ENCODE 17.8 +82.0 81970 1.9 SIN3A RAD21 RFX5 ZNF335 GLIS2 EGR2 SP3 ZBTB11 ELF1 ZNF843 ENSG00000260634 LOC105373604 GC02P127026 BIN1
GH02I127049 Enhancer 1.2 Ensembl ENCODE dbSUPER 19.2 +56.9 56882 1.6 HDGF RB1 KLF17 ZNF2 ZNF48 RAD21 ZNF335 ZNF366 ZNF143 CREM BIN1 LOC105373604 ENSG00000260634
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around BIN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BIN1 gene promoter:

Genomic Locations for BIN1 Gene

Genomic Locations for BIN1 Gene
59,378 bases
Minus strand

Genomic View for BIN1 Gene

Genes around BIN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BIN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BIN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BIN1 Gene

Proteins for BIN1 Gene

  • Protein details for BIN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Myc box-dependent-interacting protein 1
    Protein Accession:
    Secondary Accessions:
    • O00297
    • O00545
    • O43867
    • O60552
    • O60553
    • O60554
    • O60555
    • O75514
    • O75515
    • O75516
    • O75517
    • O75518
    • Q659B7
    • Q92944
    • Q99688

    Protein attributes for BIN1 Gene

    593 amino acids
    Molecular mass:
    64699 Da
    Quaternary structure:
    • Heterodimer with AMPH. Binds SH3GLB1 (By similarity). Interacts (via SH3 domain) with SYNJ1. Interacts (via SH3 domain) with DNM1. Isoform IIA interacts with CLTC. Isoform IIB does not interact with CLTC. Isoform IIC1 does not interact with CLTC. Isoform IIC2 does not interact with CLTC. Interacts with AP2A2. Interacts with AP2B1. Interacts with MYC (via N-terminal transactivation domain); the interaction requires the integrity of the conserved MYC box regions 1 and 2. Interacts with BIN2. Interacts (SH3 domain) with HCV NS5A.
    • Sequence=AAC23441.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for BIN1 Gene

    Alternative splice isoforms for BIN1 Gene

neXtProt entry for BIN1 Gene

Post-translational modifications for BIN1 Gene

No data available for DME Specific Peptides for BIN1 Gene

Domains & Families for BIN1 Gene

Gene Families for BIN1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for BIN1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with BIN1: view

No data available for UniProtKB/Swiss-Prot for BIN1 Gene

Function for BIN1 Gene

Molecular function for BIN1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in regulation of synaptic vesicle endocytosis. May act as a tumor suppressor and inhibits malignant cell transformation.

Phenotypes From GWAS Catalog for BIN1 Gene

Gene Ontology (GO) - Molecular Function for BIN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10903846
GO:0042802 identical protein binding IPI 23917616
GO:0048156 tau protein binding IPI 23399914
GO:0051015 actin filament binding IDA 26506308
GO:0070063 RNA polymerase binding IPI 16530520
genes like me logo Genes that share ontologies with BIN1: view
genes like me logo Genes that share phenotypes with BIN1: view

Human Phenotype Ontology for BIN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for BIN1 Gene

MGI Knock Outs for BIN1:

miRNA for BIN1 Gene

miRTarBase miRNAs that target BIN1

Clone Products

  • Addgene plasmids for BIN1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for BIN1 Gene

Localization for BIN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BIN1 Gene

Isoform BIN1: Nucleus.
Isoform IIA: Cytoplasm.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for BIN1 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5
plasma membrane 4
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for BIN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005635 nuclear envelope IEA --
GO:0005737 cytoplasm IDA --
GO:0005829 cytosol TAS --
GO:0015629 actin cytoskeleton TAS 9182667
genes like me logo Genes that share ontologies with BIN1: view

Pathways & Interactions for BIN1 Gene

genes like me logo Genes that share pathways with BIN1: view

Pathways by source for BIN1 Gene

1 BioSystems pathway for BIN1 Gene
2 KEGG pathways for BIN1 Gene
1 Cell Signaling Technology pathway for BIN1 Gene

Gene Ontology (GO) - Biological Process for BIN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 endocytosis IEA --
GO:0006997 nucleus organization IMP 26506308
GO:0007275 multicellular organism development IEA --
GO:0008283 cell proliferation TAS 8782822
GO:0016032 viral process IEA --
genes like me logo Genes that share ontologies with BIN1: view

No data available for SIGNOR curated interactions for BIN1 Gene

Drugs & Compounds for BIN1 Gene

(1) Drugs for BIN1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with BIN1: view

Transcripts for BIN1 Gene

Unigene Clusters for BIN1 Gene

Bridging integrator 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for BIN1

Alternative Splicing Database (ASD) splice patterns (SP) for BIN1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b · 20c ^
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - - - -
SP7: - - - - - - - - -
SP8: - - - - - - - - -
SP9: - - - - - - - - - -
SP10: - - - - - - - - - -
SP11: - - - - - - - - - - -
SP13: -
SP14: - -
SP15: - - - - - -

ExUns: 21a · 21b ^ 22a · 22b
SP1: -
SP2: -
SP3: -
SP4: -
SP5: -
SP6: -
SP7: -
SP8: -
SP9: -
SP10: -
SP11: -
SP14: -
SP15: -

Relevant External Links for BIN1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BIN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BIN1 Gene

mRNA differential expression in normal tissues according to GTEx for BIN1 Gene

This gene is overexpressed in Muscle - Skeletal (x15.8).

Protein differential expression in normal tissues from HIPED for BIN1 Gene

This gene is overexpressed in Brain (13.7), Frontal cortex (7.9), and Tonsil (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for BIN1 Gene

Protein tissue co-expression partners for BIN1 Gene

NURSA nuclear receptor signaling pathways regulating expression of BIN1 Gene:


SOURCE GeneReport for Unigene cluster for BIN1 Gene:


mRNA Expression by UniProt/SwissProt for BIN1 Gene:

Tissue specificity: Ubiquitous. Highest expression in the brain and muscle. Isoform IIA is expressed only in the brain where it is concentrated in axon initial segments and nodes of Ranvier. Isoform BIN1 is widely expressed with highest expression in skeletal muscle.

Evidence on tissue expression from TISSUES for BIN1 Gene

  • Nervous system(4.9)
  • Muscle(4.8)
  • Blood(4.5)
  • Liver(4.3)
  • Eye(2.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for BIN1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • tongue
  • vocal cord
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • finger
  • foot
  • forearm
  • hand
  • hip
  • knee
  • lower limb
  • shin
  • shoulder
  • thigh
  • toe
  • upper limb
  • wrist
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with BIN1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for BIN1 Gene

Orthologs for BIN1 Gene

This gene was present in the common ancestor of animals.

Orthologs for BIN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BIN1 33 34
  • 99.66 (n)
(Bos Taurus)
Mammalia BIN1 34
  • 96 (a)
(Canis familiaris)
Mammalia BIN1 33 34
  • 92.66 (n)
(Rattus norvegicus)
Mammalia Bin1 33
  • 90.73 (n)
(Mus musculus)
Mammalia Bin1 33 16 34
  • 90.61 (n)
(Monodelphis domestica)
Mammalia BIN1 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 42 (a)
(Gallus gallus)
Aves BIN1 33 34
  • 74.68 (n)
(Anolis carolinensis)
Reptilia BIN1 34
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia bin1 33
  • 72.12 (n)
MGC76187 33
African clawed frog
(Xenopus laevis)
Amphibia bin1-prov 33
(Danio rerio)
Actinopterygii LOC563561 33
  • 61.14 (n)
bin1 34
  • 60 (a)
BIN1 (1 of 2) 34
  • 53 (a)
fruit fly
(Drosophila melanogaster)
Insecta Amph 35 34
  • 41 (a)
(Caenorhabditis elegans)
Secernentea F58G6.1 35
  • 32 (a)
amph-1 34
  • 27 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3172 34
  • 25 (a)
Species where no ortholog for BIN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for BIN1 Gene

Gene Tree for BIN1 (if available)
Gene Tree for BIN1 (if available)

Paralogs for BIN1 Gene

Paralogs for BIN1 Gene

(2) SIMAP similar genes for BIN1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with BIN1: view

Variants for BIN1 Gene

Sequence variations from dbSNP and Humsavar for BIN1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1029519047 uncertain-significance, Autosomal recessive centronuclear myopathy 127,107,309(-) G/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1054667723 uncertain-significance, Autosomal recessive centronuclear myopathy 127,107,140(-) G/A/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1060743 conflicting-interpretations-of-pathogenicity, likely-benign, not specified, Autosomal recessive centronuclear myopathy 127,068,957(-) A/G coding_sequence_variant, synonymous_variant
rs111649895 uncertain-significance, Autosomal recessive centronuclear myopathy 127,048,444(-) G/A/T 3_prime_UTR_variant
rs112318500 conflicting-interpretations-of-pathogenicity, not specified, Autosomal recessive centronuclear myopathy 127,050,500(-) G/A/C coding_sequence_variant, intron_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for BIN1 Gene

Variant ID Type Subtype PubMed ID
dgv4064n100 CNV gain 25217958
dgv4065n100 CNV gain 25217958
dgv4066n100 CNV gain 25217958
esv2720727 CNV deletion 23290073
esv2759090 CNV gain 17122850
nsv1001064 CNV loss 25217958
nsv1005149 CNV gain 25217958
nsv10142 CNV gain 18304495
nsv2911 CNV insertion 18451855
nsv516759 CNV loss 19592680
nsv583032 CNV loss 21841781
nsv583033 CNV loss 21841781
nsv583034 CNV loss 21841781
nsv583035 CNV loss 21841781
nsv954812 CNV deletion 24416366
nsv999422 CNV gain 25217958

Variation tolerance for BIN1 Gene

Residual Variation Intolerance Score: 43% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.68; 57.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BIN1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BIN1 Gene

Disorders for BIN1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for BIN1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search BIN1 in MalaCards View complete list of genes associated with diseases


  • Myopathy, centronuclear, 2 (CNM2) [MIM:255200]: A congenital muscle disorder characterized by progressive muscular weakness and wasting involving mainly limb girdle, trunk, and neck muscles. It may also affect distal muscles. Weakness may be present during childhood or adolescence or may not become evident until the third decade of life. Ptosis is a frequent clinical feature. The most prominent histopathologic features include high frequency of centrally located nuclei in muscle fibers not secondary to regeneration, radial arrangement of sarcoplasmic strands around the central nuclei, and predominance and hypotrophy of type 1 fibers. {ECO:0000269 PubMed:17676042}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for BIN1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with BIN1: view

No data available for Genatlas for BIN1 Gene

Publications for BIN1 Gene

  1. Mutations in amphiphysin 2 (BIN1) disrupt interaction with dynamin 2 and cause autosomal recessive centronuclear myopathy. (PMID: 17676042) Nicot AS … Laporte J (Nature genetics 2007) 2 3 4 22 58
  2. The SH3 binding motif of HCV [corrected] NS5A protein interacts with Bin1 and is important for apoptosis and infectivity. (PMID: 16530520) Nanda SK … Liang TJ (Gastroenterology 2006) 3 4 22 58
  3. A role for the putative tumor suppressor Bin1 in muscle cell differentiation. (PMID: 9418903) Wechsler-Reya RJ … Prendergast GC (Molecular and cellular biology 1998) 3 4 22 58
  4. Multiple amphiphysin II splice variants display differential clathrin binding: identification of two distinct clathrin-binding sites. (PMID: 9603201) Ramjaun AR … McPherson PS (Journal of neurochemistry 1998) 3 4 22 58
  5. Identification and characterization of a nerve terminal-enriched amphiphysin isoform. (PMID: 9195986) Ramjaun AR … McPherson PS (The Journal of biological chemistry 1997) 3 4 22 58

Products for BIN1 Gene

  • Addgene plasmids for BIN1

Sources for BIN1 Gene

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