VAPB VAMP associated protein B and C [Homo sapiens (human)] - Gene

Summary

Official Symbol: VAPBprovided by HGNC
Official Full Name: VAMP associated protein B and Cprovided by HGNC
Primary source: HGNC:HGNC:12649
See related: Ensembl:ENSG00000124164 MIM:605704; AllianceGenome:HGNC:12649
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ALS8; VAP-B; VAMP-B
Summary: 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]
Expression: Ubiquitous expression in thyroid (RPKM 14.9), brain (RPKM 14.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.32

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (58389229..58451101)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (60170197..60232150)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (56964285..57026157)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

lncRNA DANCR Promotes Proliferation and Metastasis of Breast Cancer Cells Through Sponging miR-4319 and Upregulating VAPB.
Title: lncRNA DANCR Promotes Proliferation and Metastasis of Breast Cancer Cells Through Sponging miR-4319 and Upregulating VAPB.
Alteration of Vesicle-Associated Membrane Protein-Binding Protein B in alpha-Synuclein Aggregates in Lewy Body Disease.
Title: Alteration of Vesicle-Associated Membrane Protein-Binding Protein B in α-Synuclein Aggregates in Lewy Body Disease.
Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3beta.
Title: Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3β.
Sequestosome 1 Is Part of the Interaction Network of VAPB.
Title: Sequestosome 1 Is Part of the Interaction Network of VAPB.
Pathomechanisms of ALS8: altered autophagy and defective RNA binding protein (RBP) homeostasis due to the VAPB P56S mutation.
Title: Pathomechanisms of ALS8: altered autophagy and defective RNA binding protein (RBP) homeostasis due to the VAPB P56S mutation.
Role of Vesicle-Associated Membrane Protein-Associated Proteins (VAP) A and VAPB in Nuclear Egress of the Alphaherpesvirus Pseudorabies Virus.
Title: Role of Vesicle-Associated Membrane Protein-Associated Proteins (VAP) A and VAPB in Nuclear Egress of the Alphaherpesvirus Pseudorabies Virus.
Different gene expression profiles in iPSC-derived motor neurons from ALS8 patients with variable clinical courses suggest mitigating pathways for neurodegeneration.
Title: Different gene expression profiles in iPSC-derived motor neurons from ALS8 patients with variable clinical courses suggest mitigating pathways for neurodegeneration.
Disruption of endoplasmic reticulum-mitochondria tethering proteins in post-mortem Alzheimer's disease brain.
Title: Disruption of endoplasmic reticulum-mitochondria tethering proteins in post-mortem Alzheimer's disease brain.
Characterization of the amyotrophic lateral sclerosis-linked P56S mutation of the VAPB gene in Southern Brazil.
Title: Characterization of the amyotrophic lateral sclerosis-linked P56S mutation of the VAPB gene in Southern Brazil.
CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
Title: CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.

Submit: New GeneRIF Correction See all GeneRIFs (75)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Adult-onset proximal spinal muscular atrophy, autosomal dominant MedGen: C1854058 OMIM: 182980 GeneReviews: Not available	Compare labs
Amyotrophic lateral sclerosis type 8 MedGen: C1837728 OMIM: 608627 GeneReviews: Amyotrophic Lateral Sclerosis Overview	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A004M26 (e-PCR)
- UniSTS:27418

D20S430 (e-PCR), detects polymorphism
- UniSTS:42791

D20S164 (e-PCR), detects polymorphism
- UniSTS:19284

SHGC-132475 (e-PCR)
- UniSTS:173917

RH44172 (e-PCR)
- UniSTS:34708

WI-16045 (e-PCR)
- UniSTS:81562

D20S1102 (e-PCR)
- UniSTS:42141

WI-19552 (e-PCR)
- UniSTS:63904

D20S171 (e-PCR), detects polymorphism
- UniSTS:62933

STS-AA009675 (e-PCR)
- UniSTS:21995

VAPB__5060 (e-PCR)
- UniSTS:463346

D20S173 (e-PCR)
- UniSTS:18422

SHGC-32592 (e-PCR)
- UniSTS:81663

Homology

Homologs of the VAPB gene: The VAPB gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, and frog.
Orthologs from Annotation Pipeline: 445 organisms have orthologs with human gene VAPB
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables FFAT motif binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables FFAT motif binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables FFAT motif binding	IPI Inferred from Physical Interaction more info	PubMed
enables beta-tubulin binding	IDA Inferred from Direct Assay more info	PubMed
enables cadherin binding	HDA more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables microtubule binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in COPII-coated vesicle budding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in IRE1-mediated unfolded protein response	IDA Inferred from Direct Assay more info	PubMed
involved_in endoplasmic reticulum membrane organization	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in endoplasmic reticulum organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endoplasmic reticulum unfolded protein response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endoplasmic reticulum-plasma membrane tethering	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in intracellular calcium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of viral genome replication	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
NOT located_in endoplasmic reticulum exit site	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed

General protein information

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Preferred Names: vesicle-associated membrane protein-associated protein B/C

Names: VAMP (vesicle-associated membrane protein)-associated protein B and C; VAMP-associated 33 kDa protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008073.2 RefSeqGene

Range

4931..66913

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_656

mRNA and Protein(s)

NM_001195677.2 → NP_001182606.1 vesicle-associated membrane protein-associated protein B/C isoform 2

See identical proteins and their annotated locations for NP_001182606.1

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as VAPC and VAMPC) lacks three exons in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (2, also known as VAPC and VAMPC) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AF086629, AK124571, AL035455, BM968517, DA450527

Consensus CDS

CCDS56198.1

UniProtKB/Swiss-Prot

O95292

Related

ENSP00000379147.3, ENST00000395802.7

Conserved Domains (1) summary

pfam00635
Location:8 → 90

Motile_Sperm; MSP (Major sperm protein) domain
NM_004738.5 → NP_004729.1 vesicle-associated membrane protein-associated protein B/C isoform 1

See identical proteins and their annotated locations for NP_004729.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

AK023241, AK124571, AL035455, BM968517

Consensus CDS

CCDS33498.1

UniProtKB/Swiss-Prot

O95292, Q9P0H0

UniProtKB/TrEMBL

Q53XM7

Related

ENSP00000417175.1, ENST00000475243.6

Conserved Domains (1) summary

pfam00635
Location:8 → 111

Motile_Sperm; MSP (Major sperm protein) domain

RNA

NR_036633.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3, also known as VAPB-3,4) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK023241, AK124571, AK298036, AL035455, BM968517, DA450527