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Aliases for VAPB Gene

Aliases for VAPB Gene

  • VAMP Associated Protein B And C 2 3 5
  • VAMP (Vesicle-Associated Membrane Protein)-Associated Protein B And C 2 3
  • Vesicle-Associated Membrane Protein-Associated Protein B/C 3
  • VAMP-Associated 33 KDa Protein 3
  • VAMP-Associated Protein B/C 4
  • VAP-B/VAP-C 4
  • VAMP-B 3
  • VAP-B 3
  • ALS8 3

External Ids for VAPB Gene

Previous GeneCards Identifiers for VAPB Gene

  • GC20P056692
  • GC20P057602
  • GC20P057649
  • GC20P056397
  • GC20P056964
  • GC20P053747

Summaries for VAPB Gene

Entrez Gene Summary for VAPB Gene

  • The protein encoded by this gene is a type IV membrane protein found in plasma and intracellular vesicle membranes. The encoded protein is found as a homodimer and as a heterodimer with VAPA. This protein also can interact with VAMP1 and VAMP2 and may be involved in vesicle trafficking. [provided by RefSeq, Jul 2008]

GeneCards Summary for VAPB Gene

VAPB (VAMP Associated Protein B And C) is a Protein Coding gene. Diseases associated with VAPB include Spinal Muscular Atrophy, Late-Onset, Finkel Type and Amyotrophic Lateral Sclerosis 8. Among its related pathways are Metabolism and Statin Pathway. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and enzyme binding. An important paralog of this gene is VAPA.

UniProtKB/Swiss-Prot for VAPB Gene

  • Participates in the endoplasmic reticulum unfolded protein response (UPR) by inducing ERN1/IRE1 activity. Involved in cellular calcium homeostasis regulation.

Gene Wiki entry for VAPB Gene

Additional gene information for VAPB Gene

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

Genomics for VAPB Gene

GeneHancer (GH) Regulatory Elements for VAPB Gene

Promoters and enhancers for VAPB 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
GH20J058388 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 673.7 +1.2 1215 3.9 PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 CBX5 VAPB ENSG00000254419 PPP4R1L NPEPL1 GNAS-AS1 APCDD1L-DT
GH20J058407 Enhancer 1.1 Ensembl ENCODE 35.9 +19.3 19280 2.5 ELF3 PKNOX1 FOXA2 ARNT ARID4B ZBTB40 BATF IRF4 SCRT2 BCLAF1 VAPB ANKRD60 APCDD1L-DT
GH20J058432 Enhancer 0.9 Ensembl ENCODE 37.1 +44.4 44389 2.4 FOXA2 MAX RAD21 YY1 FOSL1 ZNF664 GLIS2 HNF4G FOSL2 FOS VAPB GNAS-AS1 APCDD1L-DT
GH20J058436 Enhancer 0.7 ENCODE 36.5 +48.5 48484 1.3 ELF3 TFAP4 FOXA2 SAP130 MAX ZNF384 ZNF644 KDM3A RAD21 YY1 VAPB APCDD1L-DT
GH20J058439 Enhancer 0.6 ENCODE 30.8 +50.9 50864 1.2 GTF2F1 PKNOX1 ESRRA SIN3A PAX8 RFX5 ZNF207 NFE2 MAFK ZBTB1 VAPB RAB22A PPP4R1L APCDD1L-DT
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VAPB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VAPB gene promoter:
  • SRY
  • ZIC2
  • TBP
  • Chx10
  • C/EBPalpha
  • Pbx1a
  • Cart-1
  • FOXO3
  • FOXO3a
  • FOXO3b

Genomic Locations for VAPB Gene

Genomic Locations for VAPB Gene
61,983 bases
Plus strand
61,983 bases
Plus strand

Genomic View for VAPB Gene

Genes around VAPB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for VAPB Gene

Proteins for VAPB Gene

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

    Protein Symbol:
    Recommended name:
    Vesicle-associated membrane protein-associated protein B/C
    Protein Accession:
    Secondary Accessions:
    • A2A2F2
    • O95293
    • Q9P0H0

    Protein attributes for VAPB Gene

    243 amino acids
    Molecular mass:
    27228 Da
    Quaternary structure:
    • Homodimer, and heterodimer with VAPA (PubMed:20940299). Interacts with VAMP1 and VAMP2 (PubMed:9920726, PubMed:20940299). Interacts (via MSP domain) with ZFYVE27 (PubMed:21976701, PubMed:19289470). Interacts with RMDN3 (PubMed:22131369). Interacts with KIF5A in a ZFYVE27-dependent manner (PubMed:21976701). Interacts with STARD3 (via FFAT motif) (PubMed:24105263). Interacts with STARD3NL (via FFAT motif) (PubMed:24105263).
    • (Microbial infection) Interacts with HCV protein NS5A and NS5B.

    Three dimensional structures from OCA and Proteopedia for VAPB Gene

    Alternative splice isoforms for VAPB Gene


neXtProt entry for VAPB Gene

Post-translational modifications for VAPB Gene

  • Ubiquitination at isoforms=155
  • Modification sites at PhosphoSitePlus

Other Protein References for VAPB Gene

No data available for DME Specific Peptides for VAPB Gene

Domains & Families for VAPB Gene

Gene Families for VAPB Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for VAPB Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the VAMP-associated protein (VAP) (TC 9.B.17) family.
  • Belongs to the VAMP-associated protein (VAP) (TC 9.B.17) family.
genes like me logo Genes that share domains with VAPB: view

Function for VAPB Gene

Molecular function for VAPB Gene

UniProtKB/Swiss-Prot Function:
Participates in the endoplasmic reticulum unfolded protein response (UPR) by inducing ERN1/IRE1 activity. Involved in cellular calcium homeostasis regulation.

Gene Ontology (GO) - Molecular Function for VAPB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 9920726
GO:0008017 microtubule binding IDA 18713837
GO:0019899 enzyme binding IPI 17540579
GO:0033149 FFAT motif binding IPI 24105263
GO:0042803 protein homodimerization activity IPI 9920726
genes like me logo Genes that share ontologies with VAPB: view
genes like me logo Genes that share phenotypes with VAPB: view

Human Phenotype Ontology for VAPB Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VAPB Gene

MGI Knock Outs for VAPB:
  • Vapb Vapb<tm1.2Ics>

Animal Model Products

  • Taconic Biosciences Mouse Models for VAPB

Clone Products

  • Addgene plasmids for VAPB

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for VAPB Gene

Localization for VAPB Gene

Subcellular locations from UniProtKB/Swiss-Prot for VAPB Gene

Endoplasmic reticulum membrane; Single-pass type IV membrane protein. Note=Present in mitochondria-associated membranes that are endoplasmic reticulum membrane regions closely apposed to the outer mitochondrial membrane. {ECO:0000269 PubMed:22131369}.

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 VAPB gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
cytosol 3
mitochondrion 2
nucleus 2
plasma membrane 1
cytoskeleton 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VAPB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005737 cytoplasm IDA 25468996
GO:0005783 endoplasmic reticulum IEA,IDA 15372378
GO:0005789 endoplasmic reticulum membrane IEA,TAS --
GO:0005794 Golgi apparatus IDA,IEA 16227268
genes like me logo Genes that share ontologies with VAPB: view

Pathways & Interactions for VAPB Gene

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

Pathways by source for VAPB Gene

Gene Ontology (GO) - Biological Process for VAPB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006874 cellular calcium ion homeostasis IMP,IEA 22131369
GO:0006888 ER to Golgi vesicle-mediated transport IMP 18713837
GO:0006986 response to unfolded protein IEA --
GO:0006987 obsolete activation of signaling protein activity involved in unfolded protein response IDA --
GO:0007029 endoplasmic reticulum organization IMP 18713837
genes like me logo Genes that share ontologies with VAPB: view

No data available for SIGNOR curated interactions for VAPB Gene

Drugs & Compounds for VAPB Gene

No Compound Related Data Available

Transcripts for VAPB Gene

mRNA/cDNA for VAPB Gene

Unigene Clusters for VAPB Gene

VAMP (vesicle-associated membrane protein)-associated protein B and C:
Representative Sequences:

Clone Products

  • Addgene plasmids for VAPB

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9
SP1: - - -
SP2: - - -
SP4: - - - -
SP5: - - - - - - -

Relevant External Links for VAPB Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VAPB Gene

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

Protein differential expression in normal tissues from HIPED for VAPB Gene

This gene is overexpressed in Brain (6.6).

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

Protein tissue co-expression partners for VAPB Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VAPB Gene:


SOURCE GeneReport for Unigene cluster for VAPB Gene:


mRNA Expression by UniProt/SwissProt for VAPB Gene:

Tissue specificity: Ubiquitous. Isoform 1 predominates.

Evidence on tissue expression from TISSUES for VAPB Gene

  • Nervous system(4.9)
  • Heart(4.4)
  • Liver(4.4)
  • Adrenal gland(4.3)
  • Blood(4.2)
  • Kidney(2.8)
  • Lung(2.4)
  • Muscle(2.2)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • epiglottis
  • face
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • skull
  • tongue
  • vocal cord
  • bronchus
  • clavicle
  • esophagus
  • heart
  • lung
  • scapula
  • trachea
  • biliary tract
  • liver
  • stomach
  • arm
  • digit
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • shin
  • shoulder
  • thigh
  • toe
  • upper limb
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with VAPB: view

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

Orthologs for VAPB Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for VAPB Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia VAPB 34 33
  • 99.86 (n)
(Canis familiaris)
Mammalia VAPB 34 33
  • 92.59 (n)
(Monodelphis domestica)
Mammalia VAPB 34
  • 92 (a)
(Ornithorhynchus anatinus)
Mammalia VAPB 34
  • 92 (a)
(Bos Taurus)
Mammalia VAPB 34 33
  • 91.5 (n)
(Mus musculus)
Mammalia Vapb 16 34 33
  • 87.52 (n)
(Rattus norvegicus)
Mammalia Vapb 33
  • 85.46 (n)
(Gallus gallus)
Aves VAPB 34 33
  • 83.4 (n)
(Anolis carolinensis)
Reptilia VAPB 34
  • 90 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia MGC76271 33 33
  • 74.34 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.29271 33
(Danio rerio)
Actinopterygii vapb 34 33
  • 71.49 (n)
wufa96d05 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000626 33
  • 50.35 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vap-33-1 34 35 33
  • 47.13 (n)
fan 34
  • 23 (a)
(Caenorhabditis elegans)
Secernentea vpr-1 34 33
  • 44.96 (n)
F33D11.11 35
  • 36 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SCS22 34
  • 26 (a)
SCS2 34
  • 19 (a)
Species where no ortholog for VAPB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 VAPB Gene

Gene Tree for VAPB (if available)
Gene Tree for VAPB (if available)
Evolutionary constrained regions (ECRs) for VAPB: view image

Paralogs for VAPB Gene

Paralogs for VAPB Gene

(2) SIMAP similar genes for VAPB Gene using alignment to 3 proteins:

  • E5RK64_HUMAN
  • Q53XM7_HUMAN Pseudogenes for VAPB Gene

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

Variants for VAPB Gene

Sequence variations from dbSNP and Humsavar for VAPB Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1051165027 uncertain-significance, Spinal Muscular Atrophy, Dominant, Amyotrophic Lateral Sclerosis, Dominant 58,389,177(+) A/C/T 5_prime_UTR_variant, non_coding_transcript_variant
rs1059794 likely-benign, Spinal Muscular Atrophy, Dominant, Amyotrophic Lateral Sclerosis, Dominant 58,445,172(+) G/A/C 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs114038495 likely-benign, Spinal Muscular Atrophy, Dominant, Amyotrophic Lateral Sclerosis, Dominant 58,447,801(+) A/G/T 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs115191022 likely-benign, Amyotrophic Lateral Sclerosis, Dominant, Spinal Muscular Atrophy, Dominant 58,446,906(+) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs115932469 likely-benign, Spinal Muscular Atrophy, Dominant, Amyotrophic Lateral Sclerosis, Dominant 58,450,813(+) T/G 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

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

Variant ID Type Subtype PubMed ID
nsv834019 CNV loss 17160897
nsv3428 CNV deletion 18451855
nsv1160685 CNV deletion 26073780
nsv1118919 CNV deletion 24896259
esv2722621 CNV deletion 23290073

Variation tolerance for VAPB Gene

Residual Variation Intolerance Score: 46% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.96; 19.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VAPB 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 VAPB Gene

Disorders for VAPB Gene

MalaCards: The human disease database

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

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


  • Amyotrophic lateral sclerosis 8 (ALS8) [MIM:608627]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases. {ECO:0000269 PubMed:15372378, ECO:0000269 PubMed:16891305, ECO:0000269 PubMed:20940299, ECO:0000269 PubMed:22131369}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Spinal muscular atrophy, proximal, adult, autosomal dominant (SMAPAD) [MIM:182980]: A form of spinal muscular atrophy, a neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. SMAPAD is characterized by proximal muscle weakness that begins in the lower limbs and then progresses to upper limbs, onset in late adulthood (after third decade) and a benign course. Most of the patients remain ambulatory 10 to 40 years after clinical onset. {ECO:0000269 PubMed:15372378}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for VAPB

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 VAPB: view

No data available for Genatlas for VAPB Gene

Publications for VAPB Gene

  1. Sporadic ALS is not associated with VAPB gene mutations in Southern Italy. (PMID: 16729899) Conforti FL … Quattrone A (Journal of negative results in biomedicine 2006) 3 22 44 58
  2. Characterization of amyotrophic lateral sclerosis-linked P56S mutation of vesicle-associated membrane protein-associated protein B (VAPB/ALS8). (PMID: 16891305) Kanekura K … Matsuoka M (The Journal of biological chemistry 2006) 3 4 22 58
  3. A mutation in the vesicle-trafficking protein VAPB causes late-onset spinal muscular atrophy and amyotrophic lateral sclerosis. (PMID: 15372378) Nishimura AL … Zatz M (American journal of human genetics 2004) 3 4 22 58
  4. Molecular cloning and characterization of mammalian homologues of vesicle-associated membrane protein-associated (VAMP-associated) proteins. (PMID: 9920726) Nishimura Y … Tanaka T (Biochemical and biophysical research communications 1999) 2 3 4 58
  5. STARD3 or STARD3NL and VAP form a novel molecular tether between late endosomes and the ER. (PMID: 24105263) Alpy F … Tomasetto C (Journal of cell science 2013) 3 4 58

Products for VAPB Gene

  • Addgene plasmids for VAPB

Sources for VAPB Gene

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