ATP6V0E1

ATPase H+ transporting V0 subunit e1, the group of V-type ATPase subunits|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 5:172983771-173035445

Previous symbols: [ "ATP6H", "ATP6V0E" ]

Links

ENSG00000113732

∙ NCBI:8992 ∙ OMIM:603931 ∙ HGNC:863 ∙ Uniprot:O15342 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP6V0E1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V0E1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in ATP6V0E1

This is a list of pathogenic ClinVar variants found in the ATP6V0E1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-173020257-G-T		not specified	Uncertain significance (Jul 25, 2023)	2601515
5-173020270-C-A		not specified	Uncertain significance (Mar 29, 2023)	2560921

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V0E1	protein_coding	protein_coding	ENST00000519374	3	51689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.398	0.566	125742	0	4	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.143	41	43.7	0.939	0.00000200	521
Missense in Polyphen		10	12.153	0.82287		152
Synonymous	-0.605	19	15.9	1.19	8.05e-7	153
Loss of Function	1.66	1	5.02	0.199	2.14e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Vacuolar ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.;
Pathway: Synaptic vesicle cycle - Homo sapiens (human);Phagosome - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Collecting duct acid secretion - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Signal Transduction;Transferrin endocytosis and recycling;Ion channel transport;adenosine ribonucleotides <i>de novo</i> biosynthesis;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Innate Immune System;Immune System;Transport of small molecules;superpathway of purine nucleotide salvage;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

pRec: 0.134

Intolerance Scores

loftool: 0.358
rvis_EVS: 0.04
rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

pHI: 0.171
hipred: Y
hipred_score: 0.553
ghis: 0.618

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.508

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

Gene name: Atp6v0e
Phenotype

Zebrafish Information Network

Gene name: atp6v0e1
Affected structure: retinal cone cell
Phenotype tag: abnormal
Phenotype quality: decreased length

Gene ontology

Biological process: vacuolar acidification;insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport;transmembrane transport;proton transmembrane transport
Cellular component: endosome membrane;membrane;integral component of membrane;phagocytic vesicle membrane;proton-transporting V-type ATPase, V0 domain
Molecular function: transporter activity;ATPase coupled ion transmembrane transporter activity;proton-transporting ATPase activity, rotational mechanism