Human Gene VAPB (ENST00000475243.6_4) from GENCODE V47lift37
  Description: VAMP associated protein B and C, transcript variant 1 (from RefSeq NM_004738.5)
Gencode Transcript: ENST00000475243.6_4
Gencode Gene: ENSG00000124164.16_7
Transcript (Including UTRs)
   Position: hg19 chr20:56,964,285-57,026,157 Size: 61,873 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr20:56,964,516-57,019,291 Size: 54,776 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:56,964,285-57,026,157)mRNA (may differ from genome)Protein (243 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q53XM7_HUMAN
DESCRIPTION: SubName: Full=VAMP (Vesicle-associated membrane protein)-associated protein B and C; SubName: Full=VAMP (Vesicle-associated membrane protein)-associated protein B and C, isoform CRA_b; SubName: Full=cDNA FLJ13179 fis, clone NT2RP3003918, highly similar to Vesicle-associated membrane protein-associated protein B/C;
SIMILARITY: Contains 1 MSP domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: VAPB
Diseases sorted by gene-association score: spinal muscular atrophy, late-onset, finkel type* (1650), amyotrophic lateral sclerosis 8* (1249), amyotrophic lateral sclerosis 1* (119), vapb-related amyotrophic lateral sclerosis* (100), muscular atrophy (12), amyotrophic lateral sclerosis 21 (11), lateral sclerosis (11), spinal muscular atrophy (10), spinal muscular atrophy-4 (10), amyotrophic lateral sclerosis type 14 (9), progressive bulbar palsy (8), spinal muscular atrophy-3 (6), bronchopneumonia (5), motor neuron disease (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.64 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 457.43 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -75.60231-0.327 Picture PostScript Text
3' UTR -2081.006866-0.303 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000535 - Major_sperm
IPR008962 - PapD-like
IPR016763 - Vesicle-associated_membrane

Pfam Domains:
PF00635 - MSP (Major sperm protein) domain

SCOP Domains:
49354 - PapD-like

ModBase Predicted Comparative 3D Structure on Q53XM7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006874 cellular calcium ion homeostasis
GO:0030968 endoplasmic reticulum unfolded protein response

Cellular Component:
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK023241 - Homo sapiens cDNA FLJ13179 fis, clone NT2RP3003918, highly similar to Vesicle-associated membrane protein-associated protein B/C.
AY358464 - Homo sapiens clone DNA53977 VAPB (UNQ484) mRNA, complete cds.
BC001712 - Homo sapiens VAMP (vesicle-associated membrane protein)-associated protein B and C, mRNA (cDNA clone MGC:1832 IMAGE:3543354), complete cds.
AF086628 - Homo sapiens VAMP-associated protein B (VAP-B) mRNA, complete cds.
AF086629 - Homo sapiens VAMP-associated protein C (VAP-C) mRNA, complete cds.
AK298036 - Homo sapiens cDNA FLJ59139 complete cds, highly similar to Vesicle-associated membrane protein-associated protein B/C.
AK127252 - Homo sapiens cDNA FLJ45319 fis, clone BRHIP3005801, highly similar to Homo sapiens VAMP (vesicle-associated membrane protein)-associated protein B and C (VAPB).
AF160212 - Homo sapiens VAMP-associated 33 kDa protein mRNA, complete cds.
HQ447372 - Synthetic construct Homo sapiens clone IMAGE:100070693; CCSB003756_02 VAMP (vesicle-associated membrane protein)-associated protein B and C (VAPB) gene, encodes complete protein.
KJ892716 - Synthetic construct Homo sapiens clone ccsbBroadEn_02110 VAPB gene, encodes complete protein.
KR709863 - Synthetic construct Homo sapiens clone CCSBHm_00006900 VAPB (VAPB) mRNA, encodes complete protein.
AB529043 - Synthetic construct DNA, clone: pF1KB3502, Homo sapiens VAPB gene for VAMP (vesicle-associated membrane protein)-associated protein B and C, without stop codon, in Flexi system.
CU674842 - Synthetic construct Homo sapiens gateway clone IMAGE:100018598 5' read VAPB mRNA.
BT009811 - Homo sapiens VAMP (vesicle-associated membrane protein)-associated protein B and C mRNA, complete cds.
AB209665 - Homo sapiens mRNA for VAMP-associated protein B/C variant protein.
AK123538 - Homo sapiens cDNA FLJ41544 fis, clone CERVX2002430, highly similar to Vesicle-associated membrane protein-associated protein B/C.
AL833440 - Homo sapiens mRNA; cDNA DKFZp313G0742 (from clone DKFZp313G0742).
AK128422 - Homo sapiens cDNA FLJ46565 fis, clone THYMU3040816, moderately similar to Homo sapiens VAMP (vesicle-associated membrane protein)-associated protein B and C (VAPB).
JD129696 - Sequence 110720 from Patent EP1572962.
JD168908 - Sequence 149932 from Patent EP1572962.
AK024771 - Homo sapiens cDNA: FLJ21118 fis, clone CAS05636, highly similar to AF086629 Homo sapiens VAMP-associated protein C (VAP-C) mRNA.
JD226259 - Sequence 207283 from Patent EP1572962.
JD284292 - Sequence 265316 from Patent EP1572962.
JD523298 - Sequence 504322 from Patent EP1572962.
JD024638 - Sequence 5662 from Patent EP1572962.
JD540562 - Sequence 521586 from Patent EP1572962.
JD035976 - Sequence 17000 from Patent EP1572962.
JD497265 - Sequence 478289 from Patent EP1572962.
JD424574 - Sequence 405598 from Patent EP1572962.
JD024273 - Sequence 5297 from Patent EP1572962.
JD028908 - Sequence 9932 from Patent EP1572962.
AK025720 - Homo sapiens cDNA: FLJ22067 fis, clone HEP11115F, highly similar to AF086629 Homo sapiens VAMP-associated protein C (VAP-C) mRNA.
JD495104 - Sequence 476128 from Patent EP1572962.
JD144200 - Sequence 125224 from Patent EP1572962.
JD060821 - Sequence 41845 from Patent EP1572962.
JD465544 - Sequence 446568 from Patent EP1572962.
JD272758 - Sequence 253782 from Patent EP1572962.
JD445800 - Sequence 426824 from Patent EP1572962.
JD527249 - Sequence 508273 from Patent EP1572962.
JD324188 - Sequence 305212 from Patent EP1572962.
JD260338 - Sequence 241362 from Patent EP1572962.
JD416177 - Sequence 397201 from Patent EP1572962.
JD235053 - Sequence 216077 from Patent EP1572962.
AK124571 - Homo sapiens cDNA FLJ42580 fis, clone BRACE3008491.
AK123388 - Homo sapiens cDNA FLJ41394 fis, clone BRCAN2026197.
JC506836 - Sequence 204 from Patent EP2733220.
JC737948 - Sequence 204 from Patent WO2014075939.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000475243.1, ENST00000475243.2, ENST00000475243.3, ENST00000475243.4, ENST00000475243.5, hCG_26693 , NM_004738, Q53XM7, Q53XM7_HUMAN, uc321tdx.1, uc321tdx.2, VAPB
UCSC ID: ENST00000475243.6_4
RefSeq Accession: NM_004738.5
Protein: Q53XM7

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene VAPB:
als-overview (Amyotrophic Lateral Sclerosis Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.