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

Gene Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	10312
Gene name Gene Name - the full gene name approved by the HGNC.	T cell immune regulator 1, ATPase H+ transporting V0 subunit a3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TCIRG1
Synonyms (NCBI Gene) Gene synonyms aliases	ATP6N1C, ATP6V0A3, Atp6i, OC-116kDa, OC116, OPTB1, Stv1, TIRC7, Vph1, a3
Chromosome Chromosome number	11
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	11q13.2
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a subunit of a large protein complex known as a vacuolar H+-ATPase (V-ATPase). The protein complex acts as a pump to move protons across the membrane. This movement of protons helps regulate the pH of cells and their surrounding environm

Show/Hide all(46)

SNP ID	Visualize variation	Clinical significance	Consequence
rs137853149	C>A	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant
rs137853150	G>A,C	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs137853151	G>A,T	Pathogenic	Coding sequence variant, synonymous variant, non coding transcript variant, missense variant
rs138527421	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant, non coding transcript variant, missense variant
rs139617644	G>A	Pathogenic	Splice acceptor variant
rs140963213	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs141356870	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic downstream transcript variant, non coding transcript variant, synonymous variant
rs141859450	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, upstream transcript variant, coding sequence variant, genic upstream transcript variant, 5 prime UTR variant, non coding transcript variant
rs142539969	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs145080707	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant, non coding transcript variant, missense variant
rs145144233	C>G,T	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant, non coding transcript variant
rs145718040	C>T	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, synonymous variant, downstream transcript variant, coding sequence variant, non coding transcript variant
rs150788130	C>A,T	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, intron variant, synonymous variant, coding sequence variant, non coding transcript variant
rs151180675	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, missense variant, coding sequence variant
rs183885218	C>T	Conflicting-interpretations-of-pathogenicity	Upstream transcript variant, intron variant, genic upstream transcript variant
rs371263807	C>A,T	Pathogenic	Stop gained, genic downstream transcript variant, non coding transcript variant, coding sequence variant, downstream transcript variant, synonymous variant
rs377303800	G>A	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Upstream transcript variant, splice donor variant, genic upstream transcript variant
rs377606178	C>G,T	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, downstream transcript variant, intron variant
rs587779413	C>A	Pathogenic, uncertain-significance	Genic downstream transcript variant, coding sequence variant, missense variant, non coding transcript variant, downstream transcript variant
rs745971874	G>A	Pathogenic	Synonymous variant, coding sequence variant, non coding transcript variant
rs748659068	C>T	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs751881962	A>C,T	Pathogenic, likely-pathogenic	Intron variant, upstream transcript variant, genic upstream transcript variant
rs758977199	A>C,T	Likely-pathogenic	Splice acceptor variant
rs777785526	C>T	Conflicting-interpretations-of-pathogenicity	Stop gained, missense variant, non coding transcript variant, coding sequence variant
rs886048594	GGAGCGC>-	Conflicting-interpretations-of-pathogenicity	Upstream transcript variant, genic upstream transcript variant, frameshift variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs917505107	G>A,T	Likely-pathogenic	Splice donor variant, upstream transcript variant, genic upstream transcript variant
rs1057517365	G>A	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1208311085	CCCC>-,CCC	Likely-pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, upstream transcript variant, frameshift variant, genic upstream transcript variant
rs1300297240	G>-	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, 3 prime UTR variant
rs1338631330	C>T	Likely-pathogenic, pathogenic	Coding sequence variant, genic upstream transcript variant, 5 prime UTR variant, non coding transcript variant, stop gained, upstream transcript variant
rs1439348400	G>T	Likely-pathogenic	Splice donor variant
rs1475338876	G>A	Pathogenic	Splice donor variant, genic downstream transcript variant
rs1489993984	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, stop gained
rs1554995009	C>T	Likely-pathogenic	5 prime UTR variant, stop gained, coding sequence variant, upstream transcript variant, non coding transcript variant, genic upstream transcript variant
rs1554995115	C>T	Pathogenic	5 prime UTR variant, stop gained, coding sequence variant, upstream transcript variant, non coding transcript variant, genic upstream transcript variant
rs1554997818	T>C	Likely-pathogenic	Splice donor variant
rs1554997884	G>A	Likely-pathogenic	Splice acceptor variant
rs1554997997	->A	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554998061	->GCCG	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554999205	G>C	Likely-pathogenic	Non coding transcript variant, splice donor variant
rs1554999516	->AG	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, 3 prime UTR variant
rs1554999769	->C	Likely-pathogenic	Coding sequence variant, downstream transcript variant, non coding transcript variant, frameshift variant, genic downstream transcript variant
rs1555000376	A>G	Likely-pathogenic	Splice acceptor variant, intron variant, genic downstream transcript variant
rs1590817956	G>A	Pathogenic	Genic downstream transcript variant, downstream transcript variant, non coding transcript variant, coding sequence variant, stop gained
rs1590819770	G>C	Likely-pathogenic	Splice acceptor variant, genic downstream transcript variant, intron variant
rs1590819834	->G	Likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, frameshift variant, intron variant

Show/Hide all(78)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000045	Process	Autophagosome assembly	IEA
GO:0000220	Component	Vacuolar proton-transporting V-type ATPase, V0 domain	IEA
GO:0001503	Process	Ossification	IEA
GO:0002158	Process	Osteoclast proliferation	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IEA
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	HDA	17897319
GO:0005765	Component	Lysosomal membrane	NAS	32001091
GO:0005765	Component	Lysosomal membrane	TAS
GO:0005770	Component	Late endosome	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	NAS	32001091
GO:0005886	Component	Plasma membrane	TAS	9806637, 10329006
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006874	Process	Intracellular calcium ion homeostasis	IEA
GO:0006914	Process	Autophagy	IEA
GO:0006915	Process	Apoptotic process	IEA
GO:0006954	Process	Inflammatory response	IEA
GO:0006968	Process	Cellular defense response	TAS	9806637
GO:0007035	Process	Vacuolar acidification	IBA
GO:0007035	Process	Vacuolar acidification	NAS	32001091
GO:0007039	Process	Protein catabolic process in the vacuole	IEA
GO:0007039	Process	Protein catabolic process in the vacuole	ISS
GO:0007042	Process	Lysosomal lumen acidification	NAS	32001091
GO:0008284	Process	Positive regulation of cell population proliferation	TAS	9806637
GO:0010008	Component	Endosome membrane	NAS	32001091
GO:0010008	Component	Endosome membrane	TAS
GO:0010155	Process	Regulation of proton transport	IEA
GO:0010272	Process	Response to silver ion	IEA
GO:0010467	Process	Gene expression	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0016020	Component	Membrane	IEA
GO:0016064	Process	Immunoglobulin mediated immune response	IEA
GO:0016236	Process	Macroautophagy	IEA
GO:0016236	Process	Macroautophagy	ISS
GO:0016324	Component	Apical plasma membrane	IDA	15800125
GO:0016471	Component	Vacuolar proton-transporting V-type ATPase complex	IBA
GO:0021554	Process	Optic nerve development	IEA
GO:0030010	Process	Establishment of cell polarity	IEA
GO:0030099	Process	Myeloid cell differentiation	IEA
GO:0030183	Process	B cell differentiation	IEA
GO:0030217	Process	T cell differentiation	IEA
GO:0030316	Process	Osteoclast differentiation	IEA
GO:0030667	Component	Secretory granule membrane	IEA
GO:0030670	Component	Phagocytic vesicle membrane	IEA
GO:0030670	Component	Phagocytic vesicle membrane	TAS
GO:0031529	Process	Ruffle organization	IEA
GO:0033176	Component	Proton-transporting V-type ATPase complex	NAS	33065002
GO:0033179	Component	Proton-transporting V-type ATPase, V0 domain	IEA
GO:0033365	Process	Protein localization to organelle	IEA
GO:0035709	Process	Memory T cell activation	IEA
GO:0035711	Process	T-helper 1 cell activation	IEA
GO:0042476	Process	Odontogenesis	IEA
GO:0043029	Process	T cell homeostasis	IEA
GO:0044691	Process	Tooth eruption	IEA
GO:0045335	Component	Phagocytic vesicle	IEA
GO:0045453	Process	Bone resorption	IEA
GO:0045667	Process	Regulation of osteoblast differentiation	IEA
GO:0045851	Process	PH reduction	IEA
GO:0046961	Function	Proton-transporting ATPase activity, rotational mechanism	IEA
GO:0046961	Function	Proton-transporting ATPase activity, rotational mechanism	TAS	8579597
GO:0048872	Process	Homeostasis of number of cells	IEA
GO:0050796	Process	Regulation of insulin secretion	IEA
GO:0051117	Function	ATPase binding	IBA
GO:0051452	Process	Intracellular pH reduction	IEA
GO:0051650	Process	Establishment of vesicle localization	IEA
GO:0060041	Process	Retina development in camera-type eye	IEA
GO:0061484	Process	Hematopoietic stem cell homeostasis	IEA
GO:0070166	Process	Enamel mineralization	IEA
GO:0071345	Process	Cellular response to cytokine stimulus	IEA
GO:0090383	Process	Phagosome acidification	IEA
GO:0097188	Process	Dentin mineralization	IEA
GO:0101003	Component	Ficolin-1-rich granule membrane	TAS
GO:1902600	Process	Proton transmembrane transport	IEA
GO:1902600	Process	Proton transmembrane transport	NAS	33065002
GO:1902600	Process	Proton transmembrane transport	TAS	8579597

MIM	HGNC	e!Ensembl
604592	11647	ENSG00000110719

Protein

UniProt ID

Q13488

Protein name

V-type proton ATPase 116 kDa subunit a 3 (V-ATPase 116 kDa subunit a 3) (Osteoclastic proton pump 116 kDa subunit) (OC-116 kDa) (OC116) (T-cell immune regulator 1) (T-cell immune response cDNA7 protein) (TIRC7) (Vacuolar proton translocating ATPase 116 kD

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

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01496	V_ATPase_I	27 → 825	V-type ATPase 116kDa subunit family	Family

Tissue specificity

TISSUE SPECIFICITY: Isoform long is highly expressed in osteoclastomas. Isoform short is highly expressed in thymus.

Sequence

MGSMFRSEEVALVQLFLPTAAAYTCVSRLGELGLVEFRDLNASVSAFQRRFVVDVRRCEE
LEKTFTFLQEEVRRAGLVLPPPKGRLPAPPPRDLLRIQEETERLAQELRDVRGNQQALRA
QLHQLQLHAAVLRQGHEPQLAAAHTDGASERTPLLQAPGGPHQDLRVNFVAGAVEPHKAP
ALERLLWRACRGFLIASFRELEQPLEHPVTGEPATWMTFLISYWGEQIGQKIRKITDCFH
CHVFPFLQQEEARLGALQQLQQQSQELQEVLGETERFLSQVLGRVLQLLPPGQVQVHKMK
AVYLALNQCSVSTTHKCLIAEAWCSVRDLPALQEALRDSSMEEGVSAVAHRIPCRDMPPT
LIRTNRFTASFQGIVDAYGVGRYQEVNPAPYTIITFPFLFAVMFGDVGHGLLMFLFALAM
VLAENRPAVKAAQNEIWQTFFRGRYLLLLMGLFSIYTGFIYNECFSRATSIFPSGWSVAA
MANQSGWSDAFLAQHTMLTLDPNVTGVFLGPYPFGIDPIWSLAANHLSFLNSFKMKMSVI
LGVVHMAFGVVLGVFNHVHFGQRHRLLLETLPELTFLLGLFGYLVFLVIYKWLCVWAARA
ASAPSILIHFINMFLFSHSPSNRLLYPRQEVVQATLVVLALAMVPILLLGTPLHLLHRHR
RRLRRRPADRQEENKAGLLDLPDASVNGWSSDEEKAGGLDDEEEAELVPSEVLMHQAIHT
IEFCLGCVSNTASYLRLWALSLAHAQLSEVLWAMVMRIGLGLGREVGVAAVVLVPIFAAF
AVMTVAILLVMEGLSAFLHALRLHWVEFQNKFYSGTGYKLSPFTFAATDD

Sequence length

830

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 Neutrophil degranulation Insulin receptor recycling Transferrin endocytosis and recycling Amino acids regulate mTORC1 Ion channel transport

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Osteopetrosis	Autosomal recessive osteopetrosis 1, osteopetrosis	rs1554995381, rs761918801, rs1554995330, rs137853151, rs1458295257, rs1565156743, rs1554995582, rs1385741705, rs2134438856, rs1554997884, rs1590817956, rs1554995706, rs1554995522, rs139617644, rs200851583 View all (35 more)	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Congenital Neutropenia	Neutropenia, severe congenital, 1, autosomal dominant	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (51)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acidosis Renal Tubular	Associate	12566520
Adenocarcinoma Mucinous	Associate	1928301
Adenocarcinoma of Lung	Associate	25233467
Agammaglobulinemia	Associate	19507210
alpha Thalassemia	Associate	25834820
Alzheimer Disease	Associate	30478411, 35699875
Atherosclerosis	Associate	27229898
Barrett Esophagus	Associate	20543560
Bisphosphonate Associated Osteonecrosis of the Jaw	Associate	32119750
Bone Diseases Metabolic	Associate	20424301, 24535816
Bone Marrow Failure Disorders	Associate	24535816
Bone Marrow Neoplasms	Associate	34545712
Carcinoma Basal Cell	Associate	2556449
Carcinoma Pancreatic Ductal	Stimulate	33179081
Carcinoma Squamous Cell	Associate	18398683
Cerebral Small Vessel Diseases	Associate	35699875
Cognitive Dysfunction	Associate	30478411
Diabetes Mellitus Type 2	Associate	24595071
Disease	Associate	18715141
Disseminated Intravascular Coagulation	Associate	29331583
Fractures Bone	Associate	37107657
Glioblastoma	Associate	36980184
Glioma	Associate	35266851
Hypertension Pulmonary	Associate	19507210
Inflammation	Associate	29331583
Leukemia Lymphocytic Chronic B Cell	Associate	8639849
Lung Diseases	Associate	23114595
Lung Neoplasms	Associate	20124469, 25233467
MELAS Syndrome	Associate	35699875
Neoplasms	Associate	28045487, 29475939
Neoplasms	Stimulate	8317546
Nephritis Hereditary	Associate	23371956
Nephrotic Syndrome	Associate	23114595
Neuroblastoma	Associate	20218987, 9009220
Neutropenia Severe Congenital Autosomal Recessive 3	Associate	24753205, 27229898
Osteoarthritis	Associate	24009010
Osteoma Osteoid	Associate	24108692
Osteopetrosis	Associate	12566520, 15177004, 18715141, 20424301, 20499337, 24108692, 24535816, 25829125, 27468155, 28816234, 30885997, 31949009, 34545712, 34753502, 35356978, 37107657, 39875016 View all (2 more)
Osteopetrosis Autosomal Recessive 1	Associate	19507210, 20424301, 25504019, 29237407, 31859718, 34210262, 38335662
Osteopetrosis mild autosomal recessive form	Associate	12054167, 12507890, 16118345, 18715141, 19172990, 20424301, 23280965, 24535816, 25829125, 28816234, 29237407, 31794943, 31949009, 37672091
Ovarian Neoplasms	Associate	28358117, 38238671
Prostatic Neoplasms	Associate	25137483, 27509031, 37143720
Proteinuria	Associate	23371956
Pulmonary Arterial Hypertension	Associate	25504019
Purpura Thrombocytopenic Idiopathic	Associate	24617318
Pyle disease	Associate	32119750
Renal Artery Obstruction	Associate	27229898
Severe Acute Respiratory Syndrome	Associate	25410126
Small Cell Lung Carcinoma	Associate	20124469
Squamous Cell Carcinoma of Head and Neck	Associate	19130304, 37654227
Tuberculosis Pulmonary	Associate	24898387

TCIRG1 (T cell immune regulator 1, ATPase H+ transporting V0 subunit a3)