ATP6V1D

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

Basic information

Region (hg38): 14:67294371-67360265

Previous symbols: [ "ATP6M" ]

Links

ENSG00000100554

∙ NCBI:51382 ∙ OMIM:609398 ∙ HGNC:13527 ∙ Uniprot:Q9Y5K8 ∙ 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 ATP6V1D gene.

not_specified (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1D gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015994.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V1D	protein_coding	protein_coding	ENST00000216442	9	65895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000451	0.965	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	97	134	0.725	0.00000694	1599
Missense in Polyphen		24	42.585	0.56358		550
Synonymous	0.478	42	46.1	0.910	0.00000232	469
Loss of Function	1.91	10	19.0	0.527	0.00000116	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000218	0.000217
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. 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). May play a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium. {ECO:0000250, ECO:0000269|PubMed:21844891}.;
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);Neutrophil degranulation;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: 0.163

Intolerance Scores

loftool: 0.467
rvis_EVS: -0.03
rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

pHI: 0.307
hipred: Y
hipred_score: 0.663
ghis: 0.582

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Atp6v1d
Phenotype: hematopoietic 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype;

Gene ontology

Biological process: insulin receptor signaling pathway;regulation of macroautophagy;transferrin transport;ion transmembrane transport;neutrophil degranulation;cilium assembly;protein localization to cilium;proton transmembrane transport
Cellular component: lysosomal membrane;centrosome;cytosol;plasma membrane;cilium;membrane;proton-transporting V-type ATPase complex;specific granule membrane;extracellular exosome
Molecular function: protein binding;proton-transporting ATPase activity, rotational mechanism