ATP6V1E2

ATPase H+ transporting V1 subunit E2, the group of V-type ATPase subunits

Basic information

Region (hg38): 2:46490750-46542577

Previous symbols: [ "ATP6EL2", "ATP6V1EL2" ]

Links

ENSG00000250565 ∙ NCBI:90423 ∙ OMIM:617385 ∙ HGNC:18125 ∙ Uniprot:Q96A05 ∙ 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 ATP6V1E2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1E2 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in ATP6V1E2

This is a list of pathogenic ClinVar variants found in the ATP6V1E2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-46512063-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-46512074-A-G		not specified	Uncertain significance (Nov 19, 2022)
2-46512140-T-G		not specified	Uncertain significance (Jul 05, 2023)
2-46512244-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-46512308-C-T		not specified	Uncertain significance (Jun 09, 2022)
2-46512321-C-T		not specified	Uncertain significance (May 26, 2023)
2-46512347-T-C		not specified	Uncertain significance (May 03, 2023)
2-46512452-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-46512473-C-T		not specified	Uncertain significance (Dec 13, 2023)
2-46512521-A-G		not specified	Uncertain significance (May 16, 2022)
2-46512563-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-46512620-T-C		not specified	Uncertain significance (Sep 07, 2022)
2-46512690-C-T		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V1E2	protein_coding	protein_coding	ENST00000306448	1	51808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00295	0.824	125705	0	38	125743	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.550	143	126	1.14	0.00000657	1484
Missense in Polyphen		30	29.261	1.0253		406
Synonymous	0.122	48	49.1	0.978	0.00000254	441
Loss of Function	1.12	5	8.54	0.586	6.32e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000150	0.000141
Middle Eastern	0.000381	0.000381
South Asian	0.000196	0.000196
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase essential for assembly or catalytic function. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. This isoform is essential for energy coupling involved in acidification of acrosome (By similarity). {ECO:0000250}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);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);Signal Transduction;Transferrin endocytosis and recycling;Ion channel transport;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Purine metabolism;Innate Immune System;Immune System;Transport of small molecules;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.380
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.293
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0529

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp6v1e2

Gene ontology

• Biological process: insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport
• Cellular component: acrosomal vesicle;cytosol;proton-transporting two-sector ATPase complex, catalytic domain
• Molecular function: protein binding;proton-exporting ATPase activity, phosphorylative mechanism;proton-transporting ATPase activity, rotational mechanism