ATP6V0D2

ATPase H+ transporting V0 subunit d2, the group of V-type ATPase subunits

Basic information

Region (hg38): 8:85987323-86154225

Previous symbols: [ "ATP6D2" ]

Links

ENSG00000147614

∙ NCBI:245972 ∙ OMIM:618072 ∙ HGNC:18266 ∙ Uniprot:Q8N8Y2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Ehlers-Danlos syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP6V0D2 gene.

not_specified (62 variants)
not_provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V0D2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152565.1. 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				1 clinvar		1
missense			62 clinvar	1 clinvar	1 clinvar	64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	0	0	62	2	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V0D2	protein_coding	protein_coding	ENST00000285393	8	166906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.47e-11	0.0744	125400	0	344	125744	0.00137

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.769	222	192	1.16	0.0000104	2308
Missense in Polyphen		72	65.559	1.0982		814
Synonymous	-0.700	82	74.3	1.10	0.00000426	645
Loss of Function	0.250	17	18.1	0.937	0.00000101	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000659	0.000659
Ashkenazi Jewish	0.00268	0.00258
East Asian	0.0145	0.0138
Finnish	0.00	0.00
European (Non-Finnish)	0.000243	0.000237
Middle Eastern	0.0145	0.0138
South Asian	0.000491	0.000457
Other	0.000835	0.000815

dbNSFP

Source: dbNSFP

Function: FUNCTION: Subunit of the integral membrane V0 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. May play a role in coupling of proton transport and ATP hydrolysis (By similarity). {ECO:0000250}.;
Pathway: 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);Collecting duct acid secretion - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Viral carcinogenesis - 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;Innate Immune System;Immune System;Transport of small molecules;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

pRec: 0.136

Intolerance Scores

loftool: 0.816
rvis_EVS: 0.13
rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

pHI: 0.267
hipred: N
hipred_score: 0.396
ghis: 0.422

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Atp6v0d2
Phenotype: skeleton phenotype; immune system phenotype; hematopoietic system phenotype; cellular phenotype;

Gene ontology

Biological process: vacuolar transport;vacuolar acidification;insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport
Cellular component: lysosomal membrane;early endosome;endosome membrane;membrane;apical plasma membrane;vacuolar proton-transporting V-type ATPase complex;phagocytic vesicle membrane;proton-transporting V-type ATPase, V0 domain;plasma membrane proton-transporting V-type ATPase complex;extracellular exosome
Molecular function: protein binding;proton-exporting ATPase activity, phosphorylative mechanism;proton-transporting ATPase activity, rotational mechanism