ATP6V1B2 ATPase H+ transporting V1 subunit B2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATP6V1B2provided by HGNC
Official Full Name: ATPase H+ transporting V1 subunit B2provided by HGNC
Primary source: HGNC:HGNC:854
See related: Ensembl:ENSG00000147416 MIM:606939; AllianceGenome:HGNC:854
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: DOOD; HO57; VATB; VPP3; Vma2; ZLS2; ATP6B2; ATP6B1B2
Summary: This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A, three B, and two G subunits, as well as a C, D, E, F, and H subunit. The V1 domain contains the ATP catalytic site. The protein encoded by this gene is one of two V1 domain B subunit isoforms and is the only B isoform highly expressed in osteoclasts. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 48.6), kidney (RPKM 28.3) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8p21.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (20197381..20221696)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (20462474..20486792)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (20054892..20079207)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

DOORS syndrome and a recurrent truncating ATP6V1B2 variant.
Title: DOORS syndrome and a recurrent truncating ATP6V1B2 variant.
EXOME REPORT: Novel mutation in ATP6V1B2 segregating with autosomal dominant epilepsy, intellectual disability and mild gingival and nail abnormalities.
Title: EXOME REPORT: Novel mutation in ATP6V1B2 segregating with autosomal dominant epilepsy, intellectual disability and mild gingival and nail abnormalities.
mutations in the human v-ATPase subunit ATP6V1B2 (also known as Vma2 in yeast) activate autophagic flux and maintain mTOR/TOR in an active state.
Title: Follicular lymphoma-associated mutations in vacuolar ATPase ATP6V1B2 activate autophagic flux and mTOR.
atp6v1b2 knockdown zebrafish showed developmental defects in multiple organs and systems. However, Atp6v1b2 c.1516C>T knockin mice displayed obvious cognitive defects but normal hearing and cochlear morphology. Impaired hippocampal CA1 region and weaker interaction between the V1E and B2 subunits in Atp6v1b2(Arg506X//Arg506X) mice were observed.
Title: A subunit of V-ATPases, ATP6V1B2, underlies the pathology of intellectual disability.
Serum autoantibodies to subunit B1 and subunit B2 of v-H(+) -ATPase in renal tubular acidosis patients may be responsible for impaired urinary acidification.
Title: Presence of serum autoantibodies to vacuolar H(+) -ATPase in patients with renal tubular acidosis.
Both B1 and B2 subunits of the V-ATPase are detectable in human urinary exosomes, and acid and alkali loading or distal renal tubular acidosis cause changes in the B1 but not B2 subunit abundance in urinary exosomes.
Title: Changes in V-ATPase subunits of human urinary exosomes reflect the renal response to acute acid/alkali loading and the defects in distal renal tubular acidosis.
We conclude that the effects of variation in the vacuolar ATPase may point to a new molecular mechanism that influences the long-term development of depression. This mechanism may involve dysfunction specifically in hippocampal circuitry and cognitive impairment that characterizes recurrent and chronic depression.
Title: Association of ATP6V1B2 rs1106634 with lifetime risk of depression and hippocampal neurocognitive deficits: possible novel mechanisms in the etiopathology of depression.
ATP6V1B2 is somatically mutated in 22% of follicular lymphoma tumors. Mutation hotspots found at Y371 and R400.
Title: Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation.
A missense mutation in ATP6V1B2 associated with Zimmermann-Laband syndrome.
Title: Mutations in KCNH1 and ATP6V1B2 cause Zimmermann-Laband syndrome.
The ATP6V1B2 p.Arg506X is a haploinsufficient mutation and resulted in abnormal acidification in lysosomes.
Title: De novo mutation in ATP6V1B2 impairs lysosome acidification and causes dominant deafness-onychodystrophy syndrome.

Submit: New GeneRIF Correction See all GeneRIFs (12)

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
Autosomal dominant deafness - onychodystrophy syndrome MedGen: C2675730 OMIM: 124480 GeneReviews: Not available	Compare labs
Zimmermann-Laband syndrome 2 MedGen: C4225321 OMIM: 616455 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide and gene-centric analyses of circulating myeloperoxidase levels in the charge and care consortia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See studies and variants in dbVar

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HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2 (ATP6V1B2) expression by HIV-1 Vpr in Vpr transduced macrophages	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-19010 (e-PCR)
- UniSTS:59702

D8S1949 (e-PCR)
- UniSTS:75097

ATP6V1B2_8221 (e-PCR)
- UniSTS:467572

RH118507 (e-PCR)
- UniSTS:137908

RH69321 (e-PCR)
- UniSTS:10446

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables proton transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables proton-transporting ATPase activity, rotational mechanism	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in ATP metabolic process	IEA Inferred from Electronic Annotation more info
involved_in proton transmembrane transport	TAS Traceable Author Statement more info	PubMed
involved_in regulation of macroautophagy	NAS Non-traceable Author Statement more info	PubMed
involved_in synaptic vesicle lumen acidification	IEA Inferred from Electronic Annotation more info
involved_in vacuolar acidification	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extrinsic component of synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lysosomal membrane	HDA more info	PubMed
located_in melanosome	IEA Inferred from Electronic Annotation more info
located_in microvillus	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in ruffle	IEA Inferred from Electronic Annotation more info
part_of vacuolar proton-transporting V-type ATPase, V1 domain	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: V-type proton ATPase subunit B, brain isoform

Names: ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2; H+ transporting two-sector ATPase; V-ATPase B2 subunit; V-ATPase subunit B 2; endomembrane proton pump 58 kDa subunit; testicular secretory protein Li 65; vacuolar H+-ATPase 56,000 subunit; vacuolar proton pump subunit B 2

NP_001684.2

EC 7.1.2.2

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.