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.

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.

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				1		1
missense			26	1	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding				2	26	28
Total	0	0	26	4	28

Variants in ATP6V0D2

This is a list of pathogenic ClinVar variants found in the ATP6V0D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-86048472-G-A		not specified	Uncertain significance (Mar 29, 2024)
8-86048554-A-T		not specified	Uncertain significance (May 23, 2024)
8-86048652-A-G		not specified	Uncertain significance (Nov 28, 2023)
8-86048689-C-A		not specified	Uncertain significance (Feb 01, 2023)
8-86048697-C-T		not specified	Uncertain significance (Jan 18, 2022)
8-86048698-G-A		not specified	Uncertain significance (Feb 15, 2023)
8-86048737-C-T		not specified	Uncertain significance (Oct 14, 2023)
8-86063987-C-T		not specified	Uncertain significance (May 13, 2024)
8-86064029-T-C		not specified	Uncertain significance (May 18, 2022)
8-86064156-T-C		not specified	Uncertain significance (Jun 02, 2023)
8-86064224-G-A		not specified	Uncertain significance (Jan 09, 2024)
8-86064393-C-T		not specified	Uncertain significance (Sep 14, 2022)
8-86064395-G-A		not specified	Uncertain significance (Jun 11, 2024)
8-86064423-G-C		not specified	Uncertain significance (Oct 10, 2023)
8-86064465-G-C		not specified	Uncertain significance (May 13, 2022)
8-86064476-C-T		not specified	Uncertain significance (Nov 21, 2023)
8-86064479-C-T		not specified	Uncertain significance (Nov 10, 2022)
8-86064480-G-A		not specified	Uncertain significance (Dec 21, 2022)
8-86064522-T-C		not specified	Uncertain significance (Dec 06, 2022)
8-86064561-T-C		not specified	Uncertain significance (Aug 30, 2021)
8-86069529-C-A		not specified	Uncertain significance (Dec 15, 2022)
8-86069563-C-G		not specified	Uncertain significance (Jun 22, 2023)
8-86069603-C-T		not specified	Uncertain significance (Apr 08, 2024)
8-86098925-C-T			Likely benign (Sep 15, 2020)
8-86098992-C-T		not specified	Uncertain significance (May 30, 2024)

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