Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	50617
Gene name	ATPase H+ transporting V0 subunit a4
Gene symbol	ATP6V0A4
Synonyms (NCBI Gene)	A4ATP6N1BATP6N2DRTA3RDRTA2RTA1CRTADRSTV1VPH1VPP2
Chromosome	7
Chromosome location	7q34
Summary	This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular compartments of eukaryotic cells. V-ATPase dependent acidification is necessary for such intracellular processes as protein sor

Show/Hide all (21)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28939081	C>T	Pathogenic	Missense variant, coding sequence variant
rs121908367	G>A	Pathogenic	Coding sequence variant, stop gained
rs121908369	A>T	Pathogenic	Coding sequence variant, stop gained
rs267606671	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs587776615	C>T	Pathogenic	Splice donor variant
rs587776616	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs587776617	C>T	Pathogenic	Splice acceptor variant
rs753232747	->A	Likely-pathogenic	Splice donor variant
rs754517968	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs763982675	C>A,T	Likely-pathogenic	Coding sequence variant, missense variant
rs769164245	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs779869631	G>A,C	Pathogenic	Coding sequence variant, stop gained, missense variant
rs934266733	G>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1064796145	TT>-	Pathogenic	Coding sequence variant, frameshift variant
rs1064796270	C>-	Pathogenic	Splice donor variant, coding sequence variant
rs1252623454	->T	Pathogenic	Coding sequence variant, frameshift variant
rs1443883930	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs1445362077	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1450564765	C>T	Pathogenic	Splice donor variant
rs1584907924	A>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1584934951	AGTTC>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (2)

miRTarBase ID	miRNA	Experiments	Reference
MIRT2178022	hsa-miR-3667-3p	CLIP-seq
MIRT2178023	hsa-miR-4762-5p	CLIP-seq

Show/Hide all (41)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000220	Component	Vacuolar proton-transporting V-type ATPase, V0 domain	IEA
GO:0001503	Process	Ossification	IMP	10973252
GO:0005515	Function	Protein binding	IPI	12649290, 18632794, 32814053
GO:0005765	Component	Lysosomal membrane	HDA	17897319
GO:0005768	Component	Endosome	IEA
GO:0005768	Component	Endosome	ISS
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	17360703
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	NAS	32001091
GO:0005903	Component	Brush border	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006885	Process	Regulation of pH	IMP	10973252
GO:0007035	Process	Vacuolar acidification	IBA
GO:0007605	Process	Sensory perception of sound	IMP	12414817
GO:0010008	Component	Endosome membrane	TAS
GO:0016020	Component	Membrane	IEA
GO:0016323	Component	Basolateral plasma membrane	IEA
GO:0016324	Component	Apical plasma membrane	IDA	10973252, 12649290, 15800125
GO:0016324	Component	Apical plasma membrane	IEA
GO:0016471	Component	Vacuolar proton-transporting V-type ATPase complex	IBA
GO:0016471	Component	Vacuolar proton-transporting V-type ATPase complex	IDA	10973252
GO:0016471	Component	Vacuolar proton-transporting V-type ATPase complex	IEA
GO:0030670	Component	Phagocytic vesicle membrane	TAS
GO:0030672	Component	Synaptic vesicle membrane	IEA
GO:0031526	Component	Brush border membrane	IDA	14638902
GO:0033176	Component	Proton-transporting V-type ATPase complex	NAS	33065002
GO:0033179	Component	Proton-transporting V-type ATPase, V0 domain	IEA
GO:0045177	Component	Apical part of cell	IDA	14638902, 14675051
GO:0045177	Component	Apical part of cell	IEA
GO:0046961	Function	Proton-transporting ATPase activity, rotational mechanism	IEA
GO:0051117	Function	ATPase binding	IBA
GO:0051117	Function	ATPase binding	IPI	17360703
GO:0051452	Process	Intracellular pH reduction	NAS	32001091
GO:0070062	Component	Extracellular exosome	HDA	19056867, 19199708
GO:0097254	Process	Renal tubular secretion	IMP	12414817
GO:0097401	Process	Synaptic vesicle lumen acidification	IEA
GO:1902600	Process	Proton transmembrane transport	IEA
GO:1902600	Process	Proton transmembrane transport	IEA
GO:1902600	Process	Proton transmembrane transport	IMP	10973252
GO:1902600	Process	Proton transmembrane transport	NAS	33065002

MIM	HGNC	e!Ensembl
605239	866	ENSG00000105929

Q9HBG4

Protein name

V-type proton ATPase 116 kDa subunit a 4 (V-ATPase 116 kDa isoform a 4) (Vacuolar proton translocating ATPase 116 kDa subunit a isoform 4) (Vacuolar proton translocating ATPase 116 kDa subunit a kidney isoform)

Protein function

Subunit of the V0 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (By similarity). V-ATPase is responsible

PDB

7UNF

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01496	V_ATPase_I	27 → 830	V-type ATPase 116kDa subunit family	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in adult and fetal kidney. Found in the inner ear. {ECO:0000269|PubMed:12414817}.

Sequence

MVSVFRSEEMCLSQLFLQVEAAYCCVAELGELGLVQFKDLNMNVNSFQRKFVNEVRRCES
LERILRFLEDEMQNEIVVQLLEKSPLTPLPREMITLETVLEKLEGELQEANQNQQALKQS
FLELTELKYLLKKTQDFFETETNLADDFFTEDTSGLLELKAVPAYMTGKLGFIAGVINRE
RMASFERLLWRICRGNVYLKFSEMDAPLEDPVTKEEIQKNIFIIFYQGEQLRQKIKKICD
GFRATVYPCPEPAVERREMLESVNVRLEDLITVITQTESHRQRLLQEAAANWHSWLIKVQ
KMKAVYHILNMCNIDVTQQCVIAEIWFPVADATRIKRALEQGMELSGSSMAPIMTTVQSK
TAPPTFNRTNKFTAGFQNIVDAYGVGSYREINPAPYTIITFPFLFAVMFGDCGHGTVMLL
AALWMILNERRLLSQKTDNEIWNTFFHGRYLILLMGIFSIYTGLIYNDCFSKSLNIFGSS
WSVQPMFRNGTWNTHVMEESLYLQLDPAIPGVYFGNPYPFGIDPIWNLASNKLTFLNSYK
MKMSVILGIVQMVFGVILSLFNHIYFRRTLNIILQFIPEMIFILCLFGYLVFMIIFKWCC
FDVHVSQHAPSILIHFINMFLFNYSDSSNAPLYKHQQEVQSFFVVMALISVPWMLLIKPF
ILRASHRKSQLQASRIQEDATENIEGDSSSPSSRSGQRTSADTHGALDDHGEEFNFGDVF
VHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVMNSGLQTRGWGGIVGVFI
IFAVFAVLTVAILLIMEGLSAFLHALRLHWVEFQNKFYVGDGYKFSPFSFKHILDGTAEE

Sequence length

840

Interactions

View interactions

	KEGG		Reactome
	Oxidative phosphorylation Metabolic pathways Lysosome Phagosome Synaptic vesicle cycle Collecting duct acid secretion Vibrio cholerae infection Epithelial cell signaling in Helicobacter pylori infection Tuberculosis Human papillomavirus infection Rheumatoid arthritis		ROS and RNS production in phagocytes Insulin receptor recycling Transferrin endocytosis and recycling Ion channel transport

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
ATP6V0A4-related disorder	Likely pathogenic; Pathogenic	rs748719643, rs770052600, rs2485268325, rs763982675, rs1064796145	RCV003427811 RCV003397616 RCV003906900 RCV003409596 RCV004752912	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Autosomal recessive distal renal tubular acidosis	Likely pathogenic; Pathogenic	rs1384393001, rs145809731, rs121908367, rs28939081, rs2485806968, rs1209458962, rs763982675, rs1064796270, rs769164245, rs1443883930, rs754517968, rs1450564765, rs934266733, rs1584907924, rs753232747, rs1584934951, rs1803996097 View all (2 more)	RCV001536073 RCV001797560 RCV000005457 RCV000005466 RCV003486492 View all (12 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Distal renal tubular acidosis	Pathogenic; Likely pathogenic	rs2117166533, rs1806006713, rs1443883930	RCV001849705 RCV001849706 RCV001849435	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nonpapillary renal cell carcinoma	Likely pathogenic; Pathogenic	rs587776615	RCV005887311	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Renal tubular acidosis, distal, 3, with or without sensorineural hearing loss	Likely pathogenic; Pathogenic	rs766587351, rs769417807, rs1384393001, rs1464966535, rs776867749, rs145809731, rs868326109, rs2485855824, rs121908367, rs587776615, rs587776616, rs587776617, rs2117291505, rs121908369, rs28939081 View all (18 more)	RCV005038185 RCV002264290 RCV005038254 RCV003147668 RCV002503268 View all (28 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Renal tubulopathies	Likely pathogenic; Pathogenic	rs746982385	RCV005645241	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sensorineural hearing loss disorder	Likely pathogenic; Pathogenic	rs746982385	RCV001353206	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Bailey-Bloch congenital myopathy	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Distal Renal Tubular Acidosis, Recessive	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Renal tubular acidosis with progressive nerve deafness	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENSORINEURAL HEARING LOSS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (32)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Autosomal recessive distal renal tubular acidosis	Renal Tubular Acidosis	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Breast Neoplasms	Breast neoplasm	Pubtator	30961553	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	24318988		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cutis Laxa	Cutis Laxa	BEFREE	29311258		★★★★★ ★☆☆☆☆ Found in Text Mining only
Deafness	Deafness	Pubtator	12414817	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	40775604	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Diabetic neuropathy	Pubtator	40775604	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Distal Renal Tubular Acidosis	Distal Renal Tubular Acidosis	BEFREE	12384298, 14638902, 16611712, 17595521, 19639346, 20221774, 22093743, 22854161, 23114896, 23729491, 24252324, 24564331, 25498251, 26571219, 28994037 View all (5 more)		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Distal Renal Tubular Acidosis	Distal Renal Tubular Acidosis	GENOMICS_ENGLAND_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Distal Renal Tubular Acidosis	Distal Renal Tubular Acidosis	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Encephalitis	Encephalitis	BEFREE	11737651		★★★★★ ★☆☆☆☆ Found in Text Mining only
Fanconi Syndrome	Fanconi syndrome	Pubtator	28188436, 40775604	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	38445406	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	10577919, 12414817	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	24564331, 24975934	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Calculi	Kidney stone	BEFREE	28994037		★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	26208211, 36408280, 40775604	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephrocalcinosis	Nephrocalcinosis	BEFREE	28994037		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephrocalcinosis	Nephrocalcinosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephrolithiasis	Nephrolithiasis	BEFREE	28994037		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pilocytic Astrocytoma	Astrocytoma	BEFREE	22460948		★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal tubular acidosis distal autosomal recessive	Distal renal tubular acidosis	Pubtator	10577919, 12414817, 29202719	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
RENAL TUBULAR ACIDOSIS, DISTAL, AUTOSOMAL RECESSIVE	Renal Tubular Acidosis	BEFREE	10577919, 12414817, 16611712, 20221774, 23065636, 23729491, 29202719		★★★★★ ★☆☆☆☆ Found in Text Mining only
RENAL TUBULAR ACIDOSIS, DISTAL, AUTOSOMAL RECESSIVE	Renal Tubular Acidosis	UNIPROT_DG	10973252, 12414817		★★★★★ ★☆☆☆☆ Found in Text Mining only
RENAL TUBULAR ACIDOSIS, DISTAL, AUTOSOMAL RECESSIVE	Renal Tubular Acidosis	GENOMICS_ENGLAND_DG	12414817		★★★★★ ★☆☆☆☆ Found in Text Mining only
RENAL TUBULAR ACIDOSIS, DISTAL, AUTOSOMAL RECESSIVE	Renal Tubular Acidosis	CLINVAR_DG	12414817, 16611712, 23754897, 26208211, 27247958, 29311258		★★★★★ ★☆☆☆☆ Found in Text Mining only
RENAL TUBULAR ACIDOSIS, DISTAL, AUTOSOMAL RECESSIVE	Renal Tubular Acidosis	ORPHANET_DG	23729491		★★★★★ ★☆☆☆☆ Found in Text Mining only
RENAL TUBULAR ACIDOSIS, DISTAL, AUTOSOMAL RECESSIVE	Renal Tubular Acidosis	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal Tubular Acidosis, Distal, Autosomal Recessive, with Late-Onset Sensorineural Hearing Loss	Renal Tubular Acidosis with Sensorineural Hearing Loss	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	16611712, 19639346, 23065636, 23114896, 24252324, 24564331, 24975934, 25498251, 26068435, 28188436, 31600869		★★★★★ ★☆☆☆☆ Found in Text Mining only
Sensorineural hearing loss, bilateral	Sensorineural hearing loss	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Venous Thromboembolism	Venous thromboembolism	Pubtator	39729750	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

ATP6V0A4 (ATPase H+ transporting V0 subunit a4)