ATP6V0A1

ATPase H+ transporting V0 subunit a1, the group of V-type ATPase subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:42458843-42522582

Previous symbols: [ "VPP1", "ATP6N1", "ATP6N1A" ]

Links

ENSG00000033627 ∙ NCBI:535 ∙ OMIM:192130 ∙ HGNC:865 ∙ Uniprot:Q93050 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD
• developmental and epileptic encephalopathy 104 (Strong), mode of inheritance: AD
• neurodevelopmental disorder with epilepsy and brain atrophy (Moderate), mode of inheritance: AR
• developmental and epileptic encephalopathy 104 (Strong), mode of inheritance: AD
• neurodevelopmental disorder with epilepsy and brain atrophy (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 104; Neurodevelopmental disorder with epilepsy and brain atrophy	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	33833240; 34909687

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP6V0A1 gene.

• not provided (18 variants)
• Inborn genetic diseases (12 variants)
• 6 conditions (1 variants)
• Developmental and epileptic encephalopathy 104 (1 variants)
• Global developmental delay;Seizure (1 variants)
• Global developmental delay;Seizure;Large for gestational age;Microcephaly;Hypotonia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V0A1 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			25			25
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	25	0	0

Variants in ATP6V0A1

This is a list of pathogenic ClinVar variants found in the ATP6V0A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42460911-G-A		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)
17-42460947-A-T		Global developmental delay;Seizure	Uncertain significance (Oct 30, 2019)
17-42466427-A-G		Developmental and epileptic encephalopathy 104	Likely pathogenic (Apr 04, 2024)
17-42466455-A-C		not specified	Uncertain significance (Feb 16, 2024)
17-42466492-A-G			Uncertain significance (May 18, 2023)
17-42466508-G-A		Neurodevelopmental disorder with epilepsy and brain atrophy	Pathogenic (Jul 26, 2022)
17-42470091-C-G			Uncertain significance (May 19, 2023)
17-42470107-T-G			Uncertain significance (Dec 04, 2022)
17-42470206-A-C		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
17-42477664-C-T		Inborn genetic diseases	Uncertain significance (Jan 06, 2023)
17-42477679-TG-T		Neurodevelopmental disorder with epilepsy and brain atrophy	Pathogenic (Jul 27, 2022)
17-42478484-C-A		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
17-42478530-C-T			Uncertain significance (Nov 23, 2022)
17-42478549-G-A			Uncertain significance (May 10, 2022)
17-42487320-C-T		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
17-42487368-G-T		Malignant tumor of prostate	Uncertain significance (-)
17-42490578-A-G		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
17-42494390-G-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
17-42494428-G-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
17-42494445-G-A		Inborn genetic diseases	Uncertain significance (Jun 22, 2021)
17-42494469-A-G			Uncertain significance (May 23, 2022)
17-42495034-A-G		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
17-42495059-G-A		Esophageal atresia;Pyloric stenosis	Uncertain significance (May 22, 2019)
17-42495148-T-C		Developmental and epileptic encephalopathy 104	Pathogenic (Jul 26, 2022)
17-42495164-G-A		Inborn genetic diseases	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V0A1	protein_coding	protein_coding	ENST00000264649	20	63768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00203	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.74	246	476	0.517	0.0000268	5562
Missense in Polyphen		83	223.43	0.37148		2580
Synonymous	1.04	157	174	0.900	0.00000991	1569
Loss of Function	5.56	7	49.0	0.143	0.00000300	520

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000150
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000538	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for assembly and activity of the vacuolar ATPase. Potential role in differential targeting and regulation of the enzyme for a specific organelle (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);Rheumatoid arthritis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;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;Purine metabolism;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: 0.503

Intolerance Scores

• loftool: 0.0440
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.2

Haploinsufficiency Scores

• pHI: 0.446
• hipred: Y
• hipred_score: 0.683
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.410

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp6v0a1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: atp6v0a1a
• Affected structure: neural crest cell
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: vacuolar acidification;insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport;neutrophil degranulation;toxin transport
• Cellular component: vacuolar proton-transporting V-type ATPase, V0 domain;lysosomal membrane;Golgi apparatus;cytosol;plasma membrane;endosome membrane;integral component of membrane;vacuolar proton-transporting V-type ATPase complex;nuclear speck;secretory granule membrane;phagocytic vesicle membrane;melanosome;intracellular membrane-bounded organelle;extracellular exosome;ficolin-1-rich granule membrane
• Molecular function: protein binding;proton-transporting ATPase activity, rotational mechanism;ATPase binding