ATP6V0B

protein-coding

ATPase H+ transporting V0 subunit b, the group of V-type ATPase subunits

Gene summary

This gene encodes a portion of the V0 domain of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Activity of this enzyme is necessary for such varied processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

Previous symbols:

ATP6F

MANE transcript

NM_004047.5

Inheritance

—

ClinVar variants

U:28

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr1:43,974,487-43,978,295

External References & Databases

Ensembl (ENSG00000117410)

Transcript & Mutation Effects

hg38 • Region Span ~3.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP6V0B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 14

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004047.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	28	0	0	28

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004047.5	RefSeq	NP_004038.1	8	MANE Select
ENST00000472174.7	Ensembl	ENSP00000431605.1	8	MANE Select
NM_001039457.3	RefSeq	NP_001034546.1	6	Standard
NM_001294333.2	RefSeq	NP_001281262.1	7	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
atp6v0b	Danio rerio	Structure: integument Quality: colorless abnormal

Gene / Model

Organism

Observed Phenotype

atp6v0b

Danio rerio

Structure: integument

Quality: colorless

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Synaptic vesicle cycle - Homo sapiens (human)
Phagosome - Homo sapiens (human)
Lysosome - Homo sapiens (human)
Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human)
Oxidative phosphorylation - Homo sapiens (human)

Biological Process

insulin receptor signaling pathway
ATP hydrolysis coupled proton transport
regulation of macroautophagy
transferrin transport
ion transmembrane transport

Molecular Function

transporter activity
proton-transporting ATPase activity, rotational mechanism

Cellular Component

vacuolar membrane
endosome membrane
integral component of membrane
phagocytic vesicle membrane
proton-transporting V-type ATPase, V0 domain

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000472174
Coding exons: 8
Length: 3809
Individuals with no LoFs: 125745
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125748
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.81	63	119	0.531	0.00000654	1326
Missense (PolyPhen)		27	56.644	0.47666		600
Synonymous	0.275	46	48.4	0.950	0.00000313	421
Loss of Function	3.04	0	10.8	0.00	4.59e-7	125

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Proton-conducting pore forming subunit of the membrane integral V0 complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.183
RVIS EVS: -0.05
RVIS percentile EVS: 49.39

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.633

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium