ATP6V1H

ATPase H+ transporting V1 subunit H, the group of V-type ATPase subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 8:53715543-53843558

Links

ENSG00000047249NCBI:51606OMIM:608861HGNC:18303Uniprot:Q9UI12AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP6V1H gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1H 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
21
clinvar
21
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 21 0 0

Variants in ATP6V1H

This is a list of pathogenic ClinVar variants found in the ATP6V1H region.

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

Position Type Phenotype Significance ClinVar
8-53715971-C-T not specified Uncertain significance (Jun 06, 2023)2557919
8-53715981-C-A not specified Uncertain significance (Apr 20, 2023)2539497
8-53715981-C-T not specified Uncertain significance (Jan 04, 2024)3131937
8-53743581-T-C not specified Uncertain significance (Mar 11, 2022)2275818
8-53743617-T-C not specified Uncertain significance (Feb 16, 2023)2485649
8-53743628-T-C not specified Uncertain significance (Aug 12, 2021)2244190
8-53743674-C-T not specified Uncertain significance (Jun 06, 2023)2557082
8-53756556-G-A not specified Uncertain significance (Apr 23, 2024)3329643
8-53756610-C-A not specified Uncertain significance (Sep 22, 2022)2312874
8-53769634-T-A Uncertain significance (-)1206346
8-53769743-A-G not specified Likely benign (Jul 26, 2023)2587986
8-53772113-T-C not specified Uncertain significance (Feb 13, 2024)3131942
8-53795648-C-T not specified Uncertain significance (Mar 20, 2023)2526649
8-53795733-G-A not specified Uncertain significance (May 23, 2023)2560995
8-53801841-T-C not specified Uncertain significance (Dec 28, 2022)2340656
8-53811203-G-C not specified Uncertain significance (Feb 15, 2023)2484554
8-53814729-T-C not specified Uncertain significance (Jan 30, 2024)2379173
8-53814739-C-T not specified Uncertain significance (Apr 18, 2023)2538169
8-53817496-T-C not specified Uncertain significance (Mar 02, 2023)2467764
8-53817500-C-G not specified Uncertain significance (Aug 04, 2021)2241246
8-53829452-T-C not specified Uncertain significance (May 29, 2024)3329653
8-53833024-G-A not specified Uncertain significance (Feb 10, 2022)2276128
8-53841605-T-C not specified Uncertain significance (May 26, 2024)3329633
8-53841612-G-C not specified Uncertain significance (Sep 23, 2023)3131939
8-53841648-G-C not specified Uncertain significance (Feb 27, 2023)2456781

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATP6V1Hprotein_codingprotein_codingENST00000359530 13128002
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0001451.001257280201257480.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.282122720.7810.00001513204
Missense in Polyphen70111.580.627381365
Synonymous0.8608393.60.8870.00000524856
Loss of Function3.141230.80.3890.00000159356

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005970.0000597
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.0001150.000114
Middle Eastern0.0001090.000109
South Asian0.0001010.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit H activates the ATPase activity of the enzyme and couples ATPase activity to proton flow. Vacuolar ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells, thus providing most of the energy required for transport processes in the vacuolar system (By similarity). Involved in the endocytosis mediated by clathrin-coated pits, required for the formation of endosomes. {ECO:0000250}.;
Pathway
mTOR signaling pathway - Homo sapiens (human);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);Tuberculosis - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Disease;Signal Transduction;Transferrin endocytosis and recycling;Ion channel transport;adenosine ribonucleotides <i>de novo</i> biosynthesis;Host Interactions of HIV factors;HIV Infection;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Infectious disease;Innate Immune System;Immune System;Transport of small molecules;superpathway of purine nucleotide salvage;Nef Mediated CD4 Down-regulation;Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters;The role of Nef in HIV-1 replication and disease pathogenesis;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases;purine nucleotides <i>de novo</i> biosynthesis;Nef Mediated CD8 Down-regulation (Consensus)

Recessive Scores

pRec
0.182

Intolerance Scores

loftool
0.0719
rvis_EVS
-0.73
rvis_percentile_EVS
14.02

Haploinsufficiency Scores

pHI
0.137
hipred
Y
hipred_score
0.593
ghis
0.611

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.926

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Atp6v1h
Phenotype
cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype;

Zebrafish Information Network

Gene name
atp6v1h
Affected structure
melanocyte
Phenotype tag
abnormal
Phenotype quality
translucent

Gene ontology

Biological process
endocytosis;vacuolar acidification;insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport;regulation of defense response to virus by virus;regulation of catalytic activity
Cellular component
vacuolar proton-transporting V-type ATPase, V1 domain;lysosomal membrane;cytosol;plasma membrane;extracellular exosome
Molecular function
protein binding;ATPase activity;enzyme regulator activity;proton-transporting ATPase activity, rotational mechanism