TCIRG1 T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TCIRG1provided by HGNC
Official Full Name: T cell immune regulator 1, ATPase H+ transporting V0 subunit a3provided by HGNC
Primary source: HGNC:HGNC:11647
See related: Ensembl:ENSG00000110719 MIM:604592; AllianceGenome:HGNC:11647
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: a3; Stv1; Vph1; Atp6i; OC116; OPTB1; TIRC7; ATP6N1C; ATP6V0A3; OC-116kDa
Summary: 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 environment. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, and receptor-mediated endocytosis. V-ATPase is comprised of a cytosolic V1 domain and a transmembrane V0 domain. Alternative splicing results in multiple transcript variants. Mutations in this gene are associated with infantile malignant osteopetrosis. [provided by RefSeq, May 2017]
Expression: Ubiquitous expression in bone marrow (RPKM 27.5), spleen (RPKM 26.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.2

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (68039025..68053762)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (68042666..68057403)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (67806492..67818362)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Outlining the Clinical Profile of TCIRG1 14 Variants including 5 Novels with Overview of ARO Phenotype and Ethnic Impact in 20 Egyptian Families.
Title: Outlining the Clinical Profile of TCIRG1 14 Variants including 5 Novels with Overview of ARO Phenotype and Ethnic Impact in 20 Egyptian Families.
Osteoclast rich osteopetrosis due to defects in the TCIRG1 gene.
Title: Osteoclast rich osteopetrosis due to defects in the TCIRG1 gene.
Clinical and molecular characterization of five Chinese patients with autosomal recessive osteopetrosis.
Title: Clinical and molecular characterization of five Chinese patients with autosomal recessive osteopetrosis.
TIRC7 inhibits Th1 cells by upregulating the expression of CTLA4 and STAT3 in mice with acute graftversushost disease.
Title: TIRC7 inhibits Th1 cells by upregulating the expression of CTLA‑4 and STAT3 in mice with acute graft‑versus‑host disease.
The Vacuolar H(+) ATPase alpha3 Subunit Negatively Regulates Migration and Invasion of Human Pancreatic Ductal Adenocarcinoma Cells.
Title: The Vacuolar H(+) ATPase α3 Subunit Negatively Regulates Migration and Invasion of Human Pancreatic Ductal Adenocarcinoma Cells.
Novel c.G630A TCIRG1 mutation causes aberrant splicing resulting in an unusually mild form of autosomal recessive osteopetrosis.
Title: Novel c.G630A TCIRG1 mutation causes aberrant splicing resulting in an unusually mild form of autosomal recessive osteopetrosis.
mutations in SLC29A3 and TCIRG1 in patients with Sclerosing bone dysplasias with hallmarks of dysosteosclerosis.
Title: Sclerosing bone dysplasias with hallmarks of dysosteosclerosis in four patients carrying mutations in SLC29A3 and TCIRG1.
TCIRG1 mutation is associated with osteopetrosis.
Title: CLCN7 and TCIRG1 mutations in a single family: Evidence for digenic inheritance of osteopetrosis.
The aim of this study was to develop a clinically applicable lentiviral vector expressing TCIRG1 to correct osteoclast function in Infantile malignant osteopetrosis
Title: Targeting NSG Mice Engrafting Cells with a Clinically Applicable Lentiviral Vector Corrects Osteoclasts in Infantile Malignant Osteopetrosis.
The study revealed that five of the twelve cases of autosomal recessive osteopetrosis carry at least one mutation of TCIRG1 gene.
Title: TCIRG1 and SNX10 gene mutations in the patients with autosomal recessive osteopetrosis.

Submit: New GeneRIF Correction See all GeneRIFs (45)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive osteopetrosis 1 MedGen: C1850127 OMIM: 259700 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-149479 (e-PCR)
- UniSTS:177029

MARC_5391-5392:996690342:1 (e-PCR)
- UniSTS:269500

RH70640 (e-PCR)
- UniSTS:24819

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATPase binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables proton-transporting ATPase activity, rotational mechanism	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in B cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in T cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in T cell homeostasis	IEA Inferred from Electronic Annotation more info
involved_in T-helper 1 cell activation	IEA Inferred from Electronic Annotation more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in autophagosome assembly	IEA Inferred from Electronic Annotation more info
involved_in bone resorption	IEA Inferred from Electronic Annotation more info
involved_in cellular defense response	TAS Traceable Author Statement more info	PubMed
involved_in cellular response to cytokine stimulus	IEA Inferred from Electronic Annotation more info
involved_in dentin mineralization	IEA Inferred from Electronic Annotation more info
involved_in enamel mineralization	IEA Inferred from Electronic Annotation more info
involved_in establishment of cell polarity	IEA Inferred from Electronic Annotation more info
involved_in establishment of vesicle localization	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in hematopoietic stem cell homeostasis	IEA Inferred from Electronic Annotation more info
involved_in immunoglobulin mediated immune response	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in intracellular calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
involved_in lysosomal lumen acidification	NAS Non-traceable Author Statement more info	PubMed
involved_in macroautophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in memory T cell activation	IEA Inferred from Electronic Annotation more info
involved_in optic nerve development	IEA Inferred from Electronic Annotation more info
involved_in ossification	IEA Inferred from Electronic Annotation more info
involved_in osteoclast differentiation	IEA Inferred from Electronic Annotation more info
involved_in osteoclast proliferation	IEA Inferred from Electronic Annotation more info
involved_in pH reduction	IEA Inferred from Electronic Annotation more info
involved_in phagosome acidification	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell population proliferation	TAS Traceable Author Statement more info	PubMed
involved_in protein catabolic process in the vacuole	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to organelle	IEA Inferred from Electronic Annotation more info
involved_in proton transmembrane transport	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in regulation of insulin secretion	IEA Inferred from Electronic Annotation more info
involved_in regulation of osteoblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of proton transport	IEA Inferred from Electronic Annotation more info
involved_in response to silver ion	IEA Inferred from Electronic Annotation more info
involved_in retina development in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in ruffle organization	IEA Inferred from Electronic Annotation more info
involved_in tooth eruption	IEA Inferred from Electronic Annotation more info
involved_in vacuolar acidification	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in vacuolar acidification	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	NAS Non-traceable Author Statement more info	PubMed
located_in endosome membrane	TAS Traceable Author Statement more info
located_in ficolin-1-rich granule membrane	TAS Traceable Author Statement more info
located_in late endosome	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosomal membrane	NAS Non-traceable Author Statement more info	PubMed
located_in lysosomal membrane	TAS Traceable Author Statement more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in phagocytic vesicle membrane	TAS Traceable Author Statement more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
part_of proton-transporting V-type ATPase complex	NAS Non-traceable Author Statement more info	PubMed
part_of vacuolar proton-transporting V-type ATPase complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of vacuolar proton-transporting V-type ATPase, V0 domain	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: V-type proton ATPase 116 kDa subunit a 3

Names: ATPase, H+ transporting, 116kD; T-cell immune response cDNA 7; T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a; T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3; V-ATPase 116 kDa subunit a 3; V-ATPase 116 kDa subunit a3; V-ATPase 116-kDa; V-ATPase subunit a3; V-type proton ATPase 116 kDa subunit a; V-type proton ATPase 116 kDa subunit a3; osteoclastic proton pump 116 kDa subunit; specific 116-kDa vacuolar proton pump subunit; vacuolar proton translocating ATPase 116 kDa subunit A

NP_001337988.1

EC 7.1.2.1

NP_006010.2

EC 7.1.2.1

NP_006044.1

EC 7.1.2.1

XP_047282193.1

EC 7.1.2.1

XP_047282194.1

EC 7.1.2.1

XP_047282195.1

EC 7.1.2.1

XP_047282196.1

EC 7.1.2.1

XP_047282197.1

EC 7.1.2.1

XP_047282198.1

EC 7.1.2.1

XP_047282199.1

EC 7.1.2.1

XP_054223417.1

EC 7.1.2.1

XP_054223418.1

EC 7.1.2.1

XP_054223419.1

EC 7.1.2.1

XP_054223420.1

EC 7.1.2.1

XP_054223421.1

EC 7.1.2.1

XP_054223422.1

EC 7.1.2.1

XP_054223423.1

EC 7.1.2.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007878.1 RefSeqGene

Range

4980..16884

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_115

mRNA and Protein(s)

NM_001351059.2 → NP_001337988.1 V-type proton ATPase 116 kDa subunit a 3 isoform c

Status: REVIEWED

Source sequence(s)

AP002807

Conserved Domains (1) summary

pfam01496
Location:1 → 527

V_ATPase_I; V-type ATPase 116kDa subunit family
NM_006019.4 → NP_006010.2 V-type proton ATPase 116 kDa subunit a 3 isoform a

See identical proteins and their annotated locations for NP_006010.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform a, also known as the OC116 protein because it is one of three V-ATPase 116 kD subunits. It is also referred to as the a3 isoform and is induced on osteoclast differentiation. This variant contains a unique 5' end and lacks an internal segment compared to variant 2, which results in an isoform (a) with a different N-terminus than that of isoform b.

Source sequence(s)

AP002807

Consensus CDS

CCDS8177.1

UniProtKB/Swiss-Prot

O75877, Q13488, Q8WVC5

UniProtKB/TrEMBL

A0A024R5E5, A0A8V8TM28

Related

ENSP00000265686.3, ENST00000265686.8

Conserved Domains (1) summary

pfam01496
Location:27 → 825

V_ATPase_I; V-type ATPase 116kDa subunit family
NM_006053.4 → NP_006044.1 V-type proton ATPase 116 kDa subunit a 3 isoform b

See identical proteins and their annotated locations for NP_006044.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) encodes isoform b, also known as the TCIR7 protein. This protein is expressed in T lymphocytes and is essential for normal T cell activation. This variant uses a transcription start site that is within exon 5 of variant 1, and it also includes the following intron as part of its 5' UTR. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AP002807

Consensus CDS

CCDS53670.1

UniProtKB/Swiss-Prot

Q13488

UniProtKB/TrEMBL

A0A8V8TN16

Related

ENSP00000434407.1, ENST00000532635.5

Conserved Domains (1) summary

pfam01496
Location:3 → 609

V_ATPase_I; V-type ATPase 116kDa subunit family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

68039025..68053762

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047426238.1 → XP_047282194.1 V-type proton ATPase 116 kDa subunit a 3 isoform X2

UniProtKB/Swiss-Prot

O75877, Q13488, Q8WVC5

UniProtKB/TrEMBL

A0A024R5E5, A0A8V8TM28
XM_047426243.1 → XP_047282199.1 V-type proton ATPase 116 kDa subunit a 3 isoform X6
XM_047426237.1 → XP_047282193.1 V-type proton ATPase 116 kDa subunit a 3 isoform X1

UniProtKB/TrEMBL

A0A8V8TM28
XM_047426239.1 → XP_047282195.1 V-type proton ATPase 116 kDa subunit a 3 isoform X2

UniProtKB/Swiss-Prot

O75877, Q13488, Q8WVC5

UniProtKB/TrEMBL

A0A024R5E5, A0A8V8TM28
XM_047426240.1 → XP_047282196.1 V-type proton ATPase 116 kDa subunit a 3 isoform X3

UniProtKB/TrEMBL

A0A8V8TM28
XM_047426241.1 → XP_047282197.1 V-type proton ATPase 116 kDa subunit a 3 isoform X4
XM_047426242.1 → XP_047282198.1 V-type proton ATPase 116 kDa subunit a 3 isoform X5

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

68042666..68057403

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054367443.1 → XP_054223418.1 V-type proton ATPase 116 kDa subunit a 3 isoform X2

UniProtKB/Swiss-Prot

O75877, Q13488, Q8WVC5

UniProtKB/TrEMBL

A0A024R5E5, A0A8V8TM28
XM_054367448.1 → XP_054223423.1 V-type proton ATPase 116 kDa subunit a 3 isoform X6
XM_054367442.1 → XP_054223417.1 V-type proton ATPase 116 kDa subunit a 3 isoform X1

UniProtKB/TrEMBL

A0A8V8TM28
XM_054367444.1 → XP_054223419.1 V-type proton ATPase 116 kDa subunit a 3 isoform X2

UniProtKB/Swiss-Prot

O75877, Q13488, Q8WVC5

UniProtKB/TrEMBL

A0A024R5E5, A0A8V8TM28
XM_054367445.1 → XP_054223420.1 V-type proton ATPase 116 kDa subunit a 3 isoform X3

UniProtKB/TrEMBL

A0A8V8TM28
XM_054367446.1 → XP_054223421.1 V-type proton ATPase 116 kDa subunit a 3 isoform X4
XM_054367447.1 → XP_054223422.1 V-type proton ATPase 116 kDa subunit a 3 isoform X5