ATP6V0C

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

Basic information

Region (hg38): 16:2513952-2520218

Previous symbols: [ "ATPL", "ATP6C", "ATP6L" ]

Links

ENSG00000185883 ∙ NCBI:527 ∙ OMIM:108745 ∙ HGNC:855 ∙ Uniprot:P27449 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, early onset 3, with or without developmental delay	AD	Cardiovascular	Individuals have been described as being affected by congenital cardiovascular anomalies, and awareness may enable early identification and management	Cardiovascular; Craniofacial; Dental; Neurologic	24623842; 33190975; 35600075; 36074901

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP6V0C gene.

• not provided (1 variants)
• EPILEPSY, EARLY-ONSET, 3, WITH DEVELOPMENTAL DELAY (1 variants)
• Seizure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V0C 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	1	3	7			11
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	3	9	0	0

Variants in ATP6V0C

This is a list of pathogenic ClinVar variants found in the ATP6V0C region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2514149-G-A			Uncertain significance (Dec 13, 2023)
16-2514158-G-T		not specified	Uncertain significance (Aug 30, 2022)
16-2514167-G-A		Epilepsy, early-onset, 3, with or without developmental delay	Pathogenic (Aug 14, 2023)
16-2514182-G-A			Uncertain significance (May 06, 2022)
16-2519217-G-T			Uncertain significance (May 10, 2024)
16-2519239-C-G			Uncertain significance (Jan 02, 2024)
16-2519270-GTC-G		EPILEPSY, EARLY-ONSET, 3, WITH DEVELOPMENTAL DELAY	Pathogenic (Apr 08, 2014)
16-2519296-T-G			Likely pathogenic (Nov 04, 2022)
16-2519310-C-G			Uncertain significance (Sep 01, 2019)
16-2519325-G-A		not specified	Uncertain significance (Jun 02, 2024)
16-2519326-G-C		EPILEPSY, EARLY-ONSET, 3, WITH DEVELOPMENTAL DELAY	Pathogenic (Nov 17, 2023)
16-2519391-A-T		not specified	Uncertain significance (Jul 19, 2022)
16-2519397-TACAAGTGAGCACTGG-T		Epilepsy, early-onset, 3, with or without developmental delay	Pathogenic (Aug 14, 2023)
16-2519551-C-T			Uncertain significance (Nov 04, 2022)
16-2519560-G-A		Childhood-onset epilepsy syndrome	Likely pathogenic (May 03, 2024)
16-2519560-G-C		EPILEPSY, EARLY-ONSET, 3, WITH DEVELOPMENTAL DELAY	Pathogenic (Aug 14, 2023)
16-2519570-G-GC			Uncertain significance (Mar 01, 2023)
16-2519572-G-A			Uncertain significance (Nov 04, 2022)
16-2519635-GGCACCGCCCAGCA-G		Epilepsy, early-onset, 3, with or without developmental delay	Pathogenic (Aug 14, 2023)
16-2519654-G-C		Epilepsy, early-onset, 3, with or without developmental delay	Uncertain significance (Sep 14, 2023)
16-2519662-G-A			Uncertain significance (Feb 23, 2024)
16-2519672-T-A			Likely pathogenic (Nov 04, 2022)
16-2519681-T-C			Likely pathogenic (Aug 30, 2022)
16-2519686-T-C		EPILEPSY, EARLY-ONSET, 3, WITH DEVELOPMENTAL DELAY	Pathogenic (Aug 14, 2023)
16-2519689-G-C			Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V0C	protein_coding	protein_coding	ENST00000330398	3	6349

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.742	0.248	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.99	21	109	0.194	0.00000712	987
Missense in Polyphen		4	44.649	0.089588		387
Synonymous	-0.991	62	52.8	1.17	0.00000424	346
Loss of Function	1.96	0	4.48	0.00	2.77e-7	46

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton-conducting pore forming subunit of the membrane integral V0 complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.
• 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);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: 0.161

Intolerance Scores

• loftool: 0.0894
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.437
• ghis: 0.490

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Mouse Genome Informatics

• Gene name: Atp6v0c
• 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); embryo phenotype

Zebrafish Information Network

• Gene name: atp6v0cb
• Affected structure: voltage-gated calcium channel activity
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;viral process;regulation of macroautophagy;positive regulation of Wnt signaling pathway;transferrin transport;ion transmembrane transport;neutrophil degranulation;proton transmembrane transport
• Cellular component: lysosomal membrane;plasma membrane;focal adhesion;endosome membrane;integral component of membrane;phagocytic vesicle membrane;proton-transporting V-type ATPase, V0 domain;azurophil granule membrane;extracellular exosome;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: protein binding;ubiquitin protein ligase binding;proton-transporting ATP synthase activity, rotational mechanism;proton-transporting ATPase activity, rotational mechanism