ATP6V1F

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

Basic information

Region (hg38): 7:128862856-128865847

Links

ENSG00000128524 ∙ NCBI:9296 ∙ OMIM:607160 ∙ HGNC:16832 ∙ Uniprot:Q16864 ∙ 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 ATP6V1F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1F 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	7	0	0

Variants in ATP6V1F

This is a list of pathogenic ClinVar variants found in the ATP6V1F region.

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

Position	Type	Phenotype	Significance	ClinVar
7-128862923-C-T		not specified	Uncertain significance (Sep 15, 2021)
7-128862930-C-G		not specified	Uncertain significance (Jul 11, 2023)
7-128865133-C-T		not specified	Uncertain significance (Mar 16, 2022)
7-128865379-A-T		not specified	Uncertain significance (May 14, 2024)
7-128865426-A-G		not specified	Uncertain significance (Jan 26, 2023)
7-128865429-G-A		not specified	Uncertain significance (Nov 04, 2022)
7-128865477-G-C		not specified	Uncertain significance (Dec 13, 2022)
7-128865537-C-T		not specified	Uncertain significance (Mar 30, 2024)
7-128865562-C-T		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V1F	protein_coding	protein_coding	ENST00000492758	3	3019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0147	0.701	125691	0	3	125694	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.665	76	94.2	0.807	0.00000541	962
Missense in Polyphen		19	26.318	0.72193		332
Synonymous	-0.483	43	39.2	1.10	0.00000241	297
Loss of Function	0.637	3	4.45	0.674	1.89e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - 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)

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.322
• ghis: 0.520

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp6v1f

Zebrafish Information Network

• Gene name: atp6v1f
• Affected structure: melanocyte
• Phenotype tag: abnormal
• Phenotype quality: translucent

Gene ontology

• Biological process: insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;transferrin transport;ion transmembrane transport;proton transmembrane transport
• Cellular component: cytosol;membrane;proton-transporting two-sector ATPase complex;vacuolar proton-transporting V-type ATPase complex;proton-transporting V-type ATPase, V1 domain;extracellular exosome
• Molecular function: protein binding;proton transmembrane transporter activity;ATPase activity, uncoupled;ATPase coupled ion transmembrane transporter activity;proton-transporting ATPase activity, rotational mechanism