ATP6V1H ATPase H+ transporting V1 subunit H [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATP6V1Hprovided by HGNC
Official Full Name: ATPase H+ transporting V1 subunit Hprovided by HGNC
Primary source: HGNC:HGNC:18303
See related: Ensembl:ENSG00000047249 MIM:608861; AllianceGenome:HGNC:18303
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: SFD; NBP1; VMA13; CGI-11; MSTP042; SFDbeta; SFDalpha
Summary: This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular organelles. V-ATPase-dependent organelle acidification is necessary for multiple processes including protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. The encoded protein is the regulatory H subunit of the V1 domain of V-ATPase, which is required for catalysis of ATP but not the assembly of V-ATPase. Decreased expression of this gene may play a role in the development of type 2 diabetes. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
Expression: Ubiquitous expression in brain (RPKM 40.0), kidney (RPKM 25.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8q11.23

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (53715543..53843245, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (54092959..54220638, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (54628103..54755805, complement)

Chromosome 8 - NC_000008.11 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 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?

Long Noncoding RNA lnc-TCEA1-3 Affects Osteoclastic Function by Regulating ATP6V1H.
Title: Long Noncoding RNA lnc-TCEA1-3 Affects Osteoclastic Function by Regulating ATP6V1H.
Study identified rs1481950 within ATP6V1H influencing human CSF BACE activity, which indicated that ATP6V1H gene may play some roles in the pathogenesis of neurodegenerative diseases such as Alzheimer disease.
Title: Genome-wide association study identified ATP6V1H locus influencing cerebrospinal fluid BACE activity.
These data provide evidence that partial loss of ATP6V1H function results in osteoporosis/osteopenia.
Title: Deficiency of ATP6V1H Causes Bone Loss by Inhibiting Bone Resorption and Bone Formation through the TGF-β1 Pathway.
These studies have uncovered a new, ATP6V1H-mediated pathway that regulates bone formation, and defines a new mechanism of disease that leads to bone loss. We propose that MMP9/MMP13 could be therapeutic targets for patients with this rare genetic disease.
Title: ATP6V1H Deficiency Impairs Bone Development through Activation of MMP9 and MMP13.
A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration.
Title: Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration.
ATP6V1H may represent a critical molecular mechanism involved in the development of type 2 diabetes and its compilations through its important regulatory effect on vacuolar-ATPase activity.
Title: Decreased expression of ATP6V1H in type 2 diabetes: a pilot report on the diabetes risk study in Mexican Americans.
Data show that the BCG phagosome is relatively depleted in LAMP-2, NPC1, flotillin-1, vATPase, and syntaxin 3.
Title: The Mycobacterium bovis bacille Calmette-Guerin phagosome proteome.
Our study shows that multiple mechanisms of pump dysfunction result from B1 subunit mutations with a common outcome being defective assembly
Title: The vacuolar-ATPase B1 subunit in distal tubular acidosis: novel mutations and mechanisms for dysfunction.

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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

EBI GWAS Catalog

Description
Genome-wide association of mood-incongruent psychotic bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	HIV-1 Nef-induced activation of p61Hck is required for the formation of multinucleated giant cells (MGCs), which is dependent on lysosomal proteins including vacuolar adenosine triphosphatase and proteases participated in Nef-induced MGCs	PubMed
	nef	Vacuolar ATPase subunit H (V1H) binds to the C-terminal flexible loop in HIV-1 Nef; a 15-residue oligopeptide, which is derived from positions 167-181 in Nef, specifically blocks the binding of Nef to V1H	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH46206 (e-PCR)
- UniSTS:23325

SHGC-56460 (e-PCR)
- UniSTS:50208

IB299 (e-PCR)
- UniSTS:22877

A003B09 (e-PCR)
- UniSTS:52126

D20S765E (e-PCR)
- UniSTS:154036

RH12012 (e-PCR)
- UniSTS:30902

2004 (e-PCR)
- UniSTS:38882

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
contributes_to ATP hydrolysis activity	NAS Non-traceable Author Statement more info	PubMed
enables enzyme regulator activity	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables proton-transporting ATPase activity, rotational mechanism	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Golgi lumen acidification	NAS Non-traceable Author Statement more info	PubMed
involved_in endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in endosomal lumen acidification	NAS Non-traceable Author Statement more info	PubMed
involved_in intracellular pH reduction	NAS Non-traceable Author Statement more info	PubMed
involved_in lysosomal lumen acidification	NAS Non-traceable Author Statement more info	PubMed
involved_in proton transmembrane transport	NAS Non-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	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi membrane	NAS Non-traceable Author Statement more info	PubMed
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in cytosol	TAS Traceable Author Statement more info
located_in endosome membrane	NAS Non-traceable Author Statement more info	PubMed
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 lysosomal membrane	HDA more info	PubMed
located_in lysosomal membrane	NAS Non-traceable Author Statement more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
part_of proton-transporting V-type ATPase complex	NAS Non-traceable Author Statement more info	PubMed
part_of vacuolar proton-transporting V-type ATPase, V1 domain	ISS Inferred from Sequence or Structural Similarity more info
part_of vacuolar proton-transporting V-type ATPase, V1 domain	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: V-type proton ATPase subunit H

Names: ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H; V-ATPase 50/57 kDa subunits; V-ATPase subunit H; nef-binding protein 1; protein VMA13 homolog; vacuolar ATP synthase subunit H; vacuolar ATPase subunit H; vacuolar proton pump subunit H; vacuolar proton pump subunit SFD

NP_057025.2

EC 7.1.2.2

NP_998784.1

EC 7.1.2.2

NP_998785.1

EC 7.1.2.2

XP_006716518.1

EC 7.1.2.2

XP_011515844.1

EC 7.1.2.2

XP_054216619.1

EC 7.1.2.2

XP_054216620.1

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.

mRNA and Protein(s)

NM_015941.4 → NP_057025.2 V-type proton ATPase subunit H isoform 1

See identical proteins and their annotated locations for NP_057025.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 3 encode the same isoform (1).

Source sequence(s)

AI741756, BC025275, BG197001, DA147153

Consensus CDS

CCDS6153.1

UniProtKB/Swiss-Prot

B3KMR0, Q6PK44, Q9H3E3, Q9UI12, Q9Y300

UniProtKB/TrEMBL

B3KUZ7

Related

ENSP00000352522.2, ENST00000359530.7

Conserved Domains (1) summary

cd00256
Location:17 → 465

VATPase_H; regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is ...
NM_213619.3 → NP_998784.1 V-type proton ATPase subunit H isoform 2

See identical proteins and their annotated locations for NP_998784.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AF113222, AI741756, BG197001

Consensus CDS

CCDS6154.1

UniProtKB/TrEMBL

B3KUZ7

Related

ENSP00000347359.3, ENST00000355221.7

Conserved Domains (1) summary

cd00256
Location:17 → 447

VATPase_H; regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is ...
NM_213620.3 → NP_998785.1 V-type proton ATPase subunit H isoform 1

See identical proteins and their annotated locations for NP_998785.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same isoform (1).

Source sequence(s)

AC113194, AF298777, AI741756, AK098305, BG197001, DB464555

Consensus CDS

CCDS6153.1

UniProtKB/Swiss-Prot

B3KMR0, Q6PK44, Q9H3E3, Q9UI12, Q9Y300

UniProtKB/TrEMBL

B3KUZ7

Related

ENSP00000379995.2, ENST00000396774.6

Conserved Domains (1) summary

cd00256
Location:17 → 465

VATPase_H; regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

53715543..53843245 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006716455.4 → XP_006716518.1 V-type proton ATPase subunit H isoform X1

See identical proteins and their annotated locations for XP_006716518.1

UniProtKB/TrEMBL

B3KUZ7

Conserved Domains (1) summary

cd00256
Location:17 → 447

VATPase_H; regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is ...
XM_011517542.2 → XP_011515844.1 V-type proton ATPase subunit H isoform X2

See identical proteins and their annotated locations for XP_011515844.1

Conserved Domains (1) summary

cl21727
Location:1 → 258

VATPase_H; regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is ...