ATP6V1E1

ATPase H+ transporting V1 subunit E1, the group of V-type ATPase subunits

Basic information

Region (hg38): 22:17592136-17628749

Previous symbols: [ "ATP6E", "ATP6V1E" ]

Links

ENSG00000131100 ∙ NCBI:529 ∙ OMIM:108746 ∙ HGNC:857 ∙ Uniprot:P36543 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive cutis laxa type 2C (Strong), mode of inheritance: AR
• autosomal recessive cutis laxa type 2, classic type (Supportive), mode of inheritance: AR
• autosomal recessive cutis laxa type 2C (Strong), mode of inheritance: AR
• autosomal recessive cutis laxa type 2C (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cutis laxa, autosomal recessive, type IIC	AR	Cardiovascular	The condition can include early-onset cardiomyopathy, and awareness may allow early diagnosis and management	Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal	28065471

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP6V1E1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1E1 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				18	1	19
missense		1	30	2		33
nonsense						0
start loss			1			1
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			4	7	2	13
non coding				45	39	84
Total	0	1	32	65	40

Variants in ATP6V1E1

This is a list of pathogenic ClinVar variants found in the ATP6V1E1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-17592497-T-C			Benign (Sep 11, 2018)
22-17592651-G-A			Benign (Sep 11, 2018)
22-17592681-A-G			Uncertain significance (Mar 12, 2022)
22-17592686-C-T			Likely benign (Apr 25, 2024)
22-17592687-T-A		not specified	Uncertain significance (Jan 19, 2025)
22-17592691-T-A		Autosomal recessive cutis laxa type 2C	Uncertain significance (Feb 15, 2024)
22-17592698-A-G			Likely benign (Sep 18, 2023)
22-17592703-C-T			Uncertain significance (Mar 22, 2022)
22-17592721-G-A		Autosomal recessive cutis laxa type 2C • RASopathy • Cutis laxa	Pathogenic/Likely pathogenic (Oct 21, 2024)
22-17592739-G-A			Uncertain significance (Jun 13, 2021)
22-17592745-A-G			Likely benign (Jan 24, 2023)
22-17592751-T-C			Likely benign (Sep 28, 2022)
22-17592766-A-G			Likely benign (May 10, 2019)
22-17592800-CT-C			Benign (Aug 16, 2019)
22-17592800-C-CT			Likely benign (Aug 08, 2019)
22-17592800-C-CTT			Likely benign (Aug 06, 2019)
22-17592800-C-CTTTT			Benign (Aug 10, 2019)
22-17592888-C-T			Likely benign (Dec 29, 2018)
22-17592920-T-C			Benign (Sep 22, 2018)
22-17592945-G-A			Likely benign (Oct 12, 2019)
22-17592981-G-A			Likely benign (Sep 29, 2018)
22-17592998-C-T			Likely benign (Dec 29, 2018)
22-17594513-G-A			Likely benign (Mar 09, 2024)
22-17594514-T-C			Benign (Jan 29, 2025)
22-17594539-A-G			Uncertain significance (Apr 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V1E1	protein_coding	protein_coding	ENST00000253413	9	36683

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.528	0.471	125738	0	8	125746	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	68	116	0.585	0.00000581	1500
Missense in Polyphen		5	19.43	0.25734		324
Synonymous	0.160	36	37.2	0.967	0.00000171	387
Loss of Function	2.88	3	15.1	0.199	7.26e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000582	0.0000582
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000656	0.0000653
Other	0.00	0.00

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.
• 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;adenosine ribonucleotides <i>de novo</i> biosynthesis;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Purine metabolism;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;RANKL (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.0553
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.550
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp6v1e1

Zebrafish Information Network

• Gene name: atp6v1e1b
• Affected structure: eye photoreceptor cell
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

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