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VAPB
HPA
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Annotation
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Category
Tau score
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Tau score
Brain region
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Tau score
Brain region
Category
Tau score
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Tau score
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Interacting gene (ensg_id)
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ipTM
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  • SUMMARY

  • TISSUE

  • BRAIN

  • SINGLE CELL

  • SUBCELL

  • CANCER

  • BLOOD

  • CELL LINE

  • STRUCTURE

  • INTERACTION

  • VAPB
INTERACTION INTERACTION METABOLIC PATHWAYS Show tissue menu
TRANSPORT REACTIONS
Protein interactions
Protein interactions
Methods
Human metabolism
Metabolic proteins
Methods
GENERAL INFORMATIONi

General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.

Gene namei

Official gene symbol, which is typically a short form of the gene name, according to HGNC.

VAPB
Synonyms ALS8, VAP-B, VAP-C
Gene descriptioni

Full gene name according to HGNC.

VAMP associated protein B and C
Protein classi

Assigned HPA protein class(es) for the encoded protein(s).

Read more
Disease related genes
Human disease related genes
Metabolic proteins
Potential drug targets
Transporters
Predicted locationi

All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions.

  • Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached.
  • Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s).

The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.

Membrane, Intracellular
Protein evidence Evidence at protein level (all genes)

HUMAN PROTEIN ATLAS INFORMATIONi

Summary of RNA expression analysis and annotation data generated within the Human Protein Atlas project.

Single cell type
expression clusteri

The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.

Platelets - Hemostasis (mainly)
Single cell type specificityi

The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.

Cell type enhanced (Platelets)
Tissue expression
cluster (RNA)i

The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.

Non-specific - Basic cellular processes (mainly)
Tissue specificity (RNA)i

The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected.

Low tissue specificity
Subcellular locationi

Main subcellular location based on data generated in the subcellular section of the Human Protein Atlas.

Localized to the Endoplasmic reticulum
Secretome annotationi

All genes with at least one predicted secreted isoform have been annotated and classified with the aim to determine if the corresponding protein(s) are:

  • secreted into blood
  • locally secreted
  • or actually being attached to membrane or retained in intracellular locations like mitochondria, endoplasmatic reticulum (ER), Golgi apparatus or lysosomes.
Not available
GENE INFORMATIONi

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

Chromosome 20
Cytoband q13.32
Chromosome location (bp) 58389229 - 58451101
Number of transcriptsi

Number of protein-coding transcripts from the gene as defined by Ensembl.

2
Ensembl ENSG00000124164 (version 109)
Entrez gene 9217
HGNC HGNC:12649
UniProt O95292
GeneCards VAPB
ASSAYSi

Links to data of the different assays available in the Structure & Interaction resource of the Human Protein Atlas. Click on the miniature images to directly get to the respective section.

Interaction Metabolic
INTERACTIONi

In the Interaction part of this page network plots showing the gene's first-level interaction partners according to four different datasets are displayed, including a consensus network plot showing only interactions present in at least two of the datasets. By clicking on nodes the network can be expanded. In the network plots the nodes represent genes and edge color represent the number of datasets the interaction belongs to. In-house generated AlphaFold 3 predicted 3D structures for interactions in the consensus network are displayed by clicking on the blue symbols on the edges.

The highlight bar in the top of the plot can be used to color the nodes according to subcellular location (based on data in the Subcellular section), predicted location (based on signalpeptide and transmembrane region predictions), tissue specificity (based on RNA tissue expression profiles) or proteinclass. For genes categorised as single cell type or group specific the option to highlight interaction partners expressed in the same cell type will also be available in the highlight bar.

Custom highlighting of nodes is possible using the top left Filter option in which a query of choice can be built to for example label all nodes that are tissue enriched in both human and mouse brain or those that belongs to a certain tissue expression cluster. The expression cluster for the gene is stated in the box Human Protein Atlas Information above the network plot. Click on Filter in the top left in the plot to find the query builder and some example queries.

Interactions included are direct interaction and physical associations with high and medium confidence from IntAct, physical multivalidated interactions from BioGRID, interactions with>75% probability from BioPlex and significant physical interactions from OpenCell.

Filter menu »
Fields »
e.g. Brain enriched, Localized to mitochondria, Non-specific - Basic cellular processes

Field
Term
Gene name
Class
Subclass
Category
Keyword
Chromosome
External id
Tissue
Cell type
Expression
Antibody panel
Tissue
Main location
Patient ID
Annotation
Tissue
Category
Tau score
Cluster
Reliability
Brain region
Category
Tau score
Brain region
Category
Tau score
Brain region
Category
Tau score
Cluster
Reliability
Tissue
Cell type
Enrichment
Cell type
Category
Tau score
Cell type group
Category
Tau score
Cell type
Category
Tau score
Cell type
Category
Tau score
Cell lineage
Category
Tau score
Cluster
Cluster
Location
Searches
Location
Cell line
Class
Type
Phase
Reliability
Cancer
Prognosis
Cancer
Category
Cancer
Category
Tau score
Cluster
Variants
Interacting gene (ensg_id)
Type
Number of interactions
Pathway
ipTM
Category
Category
Category
Category
Validation
Validation
Validation
Validation
Antibodies
Data type
Column


Consensus
IntAct
BioGrid
OpenCell
BioPlex
Highlight:
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Subcell location
Predicted location
Cell type specificity
Protein class

Non-commercial use only, subject to AlphaFold3 Output Terms of Use

Interaction:
Color scheme:
Confidence
Antibodies
Interactor
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PAE plot
Number of interactions: 45
Interaction# Consensus# IntAct# BioGrid# OpenCell# BioPlex
ACBD420230
ACBD5201220
AFTPH511060
AKAP11731249
ARHGEF128317150
BCAP31231369304
CANX130824238124
CFTR3410323600
CKAP492651225
DDOST266541080
EMD167294120
ESYT115563310
ESYT24236120
FAM83G42661
GET35321054
LSG1209190
MIGA220322
OSBP638177
OSBPL1021234
OSBPL1131640
OSBPL1A36500
OSBPL214300
OSBPL37221270
OSBPL630840
OSBPL9331050
PIGK428619
PITPNM121420
PRKACA254266250
PRKAR1A8153149
RAB3GAP130571
RAB3GAP230570
RASSF19112930
RMDN2212320
RMDN36241940
SACM1L926152023
SEC635041518
SSR44014320
STK42317947247
TTC1481628
TTC39B11100
USP203382101
VAPA74401141400
VPS13A30960
VPS13C608120
WDR4452680
Show allShow less
Highlight:
Off
Subcell location
Predicted location
Cell type specificity
Protein class

Number of interactions: 33 View all protein interaction data in IntAct
Interaction# Consensus# IntAct# BioGrid# OpenCell# BioPlex
AQP60264000
CD79A01444018
CFTR3410323600
CYB561049000
CYBRD1019102
EBAG9023310
EBP0159311
ELOVL4079000
EMD167294120
FAM174A1312098
GPR25027000
HSD17B130104006
JAGN11102430
KRTAP9-21123200
OSBPL1A36500
OSBPL214300
PTGES015000
REEP41293121315
RETREG3109113035
RMDN2212320
RNASEK022000
SCN3B3944027
SDCBP62422600
SKIC81830291722
TMEM101011013
TMEM25204001
TMX23131340
TTC39B11100
USP203382101
VAPA74401141400
YIF1A566550
ZBTB22010000
ZDHHC15047300
Show allShow less
Highlight:
Off
Subcell location
Predicted location
Cell type specificity
Protein class

Number of interactions: 80
Interaction# Consensus# IntAct# BioGrid# OpenCell# BioPlex
ACBD420230
ACBD5201220
AFTPH511060
AKAP11731249
ALK1510300
ARHGEF128317150
BAG68116960
BCAP31231369304
CANX130824238124
CFTR3410323600
CKAP492651225
DDOST266541080
EMD167294120
ERBB2325012000
ESYT115563310
ESYT24236120
FAF1576005
FAM83G42661
GET35321054
KRAS115414160
LMNA1754239323
LSG1209190
MARCHF52253301
MIGA220322
MTNR1A271700
NDUFS45132010
NTRK15613400
OSBP638177
OSBP221321
OSBPL1021234
OSBPL1131640
OSBPL1A36500
OSBPL214300
OSBPL37221270
OSBPL630840
OSBPL9331050
PHB12713010
PIGK428619
PITPNM121420
PPT1142510
PRKACA254266250
PRKACB152800
PRKAR1A8153149
PTPN12691631
RAB11A21112054713
RAB3GAP130571
RAB3GAP230570
RAB9A629045
RASSF19112930
RASSF3413720
RB1CC19842120
RMDN2212320
RMDN36241940
ROS1111000
RPN233399602
SACM1L926152023
SEC635041518
SLC22A1500701
SLC35C211400
SLC39A14001900
SLC39A8001020
SLC6A154525110
SNCA2412615400
SQSTM1324031220
SSR44014320
STARD3153121
STK42317947247
STX1A8962600
STX1B121400
STX420373166
TACC15102100
TGOLN20310200
TTC1481628
TTC39B11100
UBL4A6102746
USP203382101
VAPA74401141400
VPS13A30960
VPS13C608120
WDR4452680
Show allShow less
Highlight:
Off
Subcell location
Predicted location
Cell type specificity
Protein class

Number of interactions: 79
Interaction# Consensus# IntAct# BioGrid# OpenCell# BioPlex
ACBD420230
ACBD5201220
AFTPH511060
AKAP11731249
ALDH3B10162160
ARHGEF128317150
ASPH41131049
ATP2A3002120
BCAP31231369304
CANX130824238124
CAPZB10061336660
CBX5295988924
CCDC4715750550
CISD24585153
CKAP492651225
COIL163733617
COPA14240780
COPB2131291224
COPE193289213
DDOST266541080
DEGS110141
DHRS712170
EMD167294120
ERLIN19121898
ESYT115563310
ESYT24236120
FAM83G42661
GDPD100030
GET35321054
GNB12213523018
GNG5377910
LBR77262122
LNPK011670
LSG1209190
MIGA220322
NSDHL337204
OSBP638177
OSBPL1021234
OSBPL1131640
OSBPL37221270
OSBPL630840
OSBPL9331050
OST4233910
PGRMC1211852834
PIGK428619
PITPNM121420
PRKACA254266250
PRKAR1A8153149
RAB3GAP130571
RAB3GAP230570
RASSF19112930
RMDN2212320
RMDN36241940
RTN38816190
RTN4231345660
SACM1L926152023
SCFD1191274715
SEC635041518
SELENOI00060
SOAT13514212
SPCS32431320
SSR44014320
STK42317947247
TECR32217100
TMED101782510120
TTC1481628
TUBA1B224494613
UBXN79223221
VAPA74401141400
VPS13A30960
VPS13C608120
WDR4452680
YWHAB183933372450
YWHAE23512338332412
YWHAG25427143322213
YWHAH130363951446
YWHAQ9061318796
YWHAZ2221643483248
ZMPSTE24126716
Show allShow less
VAPB has no defined protein interactions in BioPlex.
METABOLIC SUMMARYi

In this summary the pathway/subsystems to which the gene belongs is shown together with the associated cellular compartment for the reactions based on metabolite information. The number of proteins and metabolites in the pathway is shown as well as the number of reactions for the selected gene. By clicking on a pathway in the summary table the associated metabolic network map is shown, together with a gene-tissue heatmap that shows the expression of genes in that pathway in different tissues.

Gene VAPB is associated with 1 reactions in 1 different subsystems, and present in the compartments: Cytosol, Endoplasmic reticulum. Provided by metabolicatlas.org
Pathway / Subsystem Subsystem-associated compartments # proteins # metabolites # reactions for
this protein
Transport reactions Cytosol, Extracellular, Lysosome, Peroxisome, Mitochondria, Golgi apparatus, Endoplasmic reticulum, Nucleus, Inner mitochondria 563 1599 1
PROTEIN INFORMATIONi

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The Splice variant identifier links to the Ensembl website protein summary for the selected splice variant. The data in the Swissprot and TrEMBL columns links to corresponding pages in the UniProt database.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide and number of predicted transmembrane region(s) according to in-house majority decision methods based on sets of predictors are also reported.

Splice variant SwissProt TrEMBL Protein class Length & mass Signal peptide
(predicted)
Transmembrane regions
(predicted)
VAPB-202 O95292
Metabolic proteins
Transporters
Predicted intracellular proteins
Disease related genes
Potential drug targets
Human disease related genes
Mapped to neXtProt
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
99 aa
11.2 kDa
No 0
VAPB-204 O95292
Q53XM7
Metabolic proteins
Transporters
Predicted membrane proteins
Disease related genes
Potential drug targets
Human disease related genes
Mapped to neXtProt
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
243 aa
27.2 kDa
No 1

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