TCIRG1

gene
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Also known as TIRC7OC-116OC116ATP6N1CAtp6ia3ATP6V0A3

Summary

TCIRG1 (T cell immune regulator 1, ATPase H+ transporting V0 subunit a3, HGNC:11647) is a protein-coding gene on chromosome 11q13.2, encoding V-type proton ATPase 116 kDa subunit a 3 (Q13488). 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.

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.

Source: NCBI Gene 10312 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): autosomal recessive osteopetrosis 1 (Definitive, ClinGen) — +4 more curated relationships
  • GWAS associations: 3
  • Clinical variants (ClinVar): 1,777 total — 103 pathogenic, 115 likely-pathogenic
  • Phenotypes (HPO): 127
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_006019

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11647
Approved symbolTCIRG1
NameT cell immune regulator 1, ATPase H+ transporting V0 subunit a3
Location11q13.2
Locus typegene with protein product
StatusApproved
AliasesTIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3
Ensembl geneENSG00000110719
Ensembl biotypeprotein_coding
OMIM604592
Entrez10312

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 9 retained_intron, 8 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000265686, ENST00000524598, ENST00000524870, ENST00000525516, ENST00000525724, ENST00000527530, ENST00000528981, ENST00000529364, ENST00000529657, ENST00000530063, ENST00000530449, ENST00000530802, ENST00000532635, ENST00000533005, ENST00000533947, ENST00000534673, ENST00000698254, ENST00000698255, ENST00000698256, ENST00000698257, ENST00000698258, ENST00000698259

RefSeq mRNA: 3 — MANE Select: NM_006019 NM_001351059, NM_006019, NM_006053

CCDS: CCDS53670, CCDS8177

Canonical transcript exons

ENST00000265686 — 20 exons

ExonStartEnd
ENSE000009044646804126868041388
ENSE000011172346804337168043497
ENSE000011668856805074168050895
ENSE000012701486804294668043031
ENSE000013630966803902568039119
ENSE000034609796804788268047972
ENSE000034712386804996268050066
ENSE000035004016804743368047572
ENSE000035337306804966368049788
ENSE000035586026804381468043907
ENSE000035601316804495868045102
ENSE000035606556805048768050664
ENSE000035613266804413268044344
ENSE000035865836804175368041831
ENSE000036084796804764768047804
ENSE000036252766804264368042863
ENSE000036305486804357168043653
ENSE000036558656805013768050254
ENSE000036705826804887968048997
ENSE000036903046804908168049294

Expression profiles

Bgee: expression breadth ubiquitous, 148 present calls, max score 99.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.6843 / max 684.2413, expressed in 1790 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
11551829.85111776
1155171.89091100
1155210.7958311
1155190.092220
1155200.054421

Top tissues by expression

158 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009499.52gold quality
bloodUBERON:000017899.36gold quality
spleenUBERON:000210699.31gold quality
body of pancreasUBERON:000115099.30gold quality
right adrenal gland cortexUBERON:003582799.01gold quality
right adrenal glandUBERON:000123398.99gold quality
left adrenal gland cortexUBERON:003582598.89gold quality
left adrenal glandUBERON:000123498.82gold quality
endocervixUBERON:000045898.69gold quality
mucosa of stomachUBERON:000119998.62gold quality
small intestine Peyer’s patchUBERON:000345498.51gold quality
upper lobe of left lungUBERON:000895298.44gold quality
right lungUBERON:000216798.41gold quality
mucosa of transverse colonUBERON:000499198.36gold quality
monocyteCL:000057698.30gold quality
right uterine tubeUBERON:000130298.23gold quality
body of uterusUBERON:000985398.21gold quality
left uterine tubeUBERON:000130398.20gold quality
leukocyteCL:000073898.14gold quality
vermiform appendixUBERON:000115498.10gold quality
fundus of stomachUBERON:000116098.10gold quality
small intestineUBERON:000210898.09gold quality
transverse colonUBERON:000115798.04gold quality
body of stomachUBERON:000116198.04gold quality
ectocervixUBERON:001224997.90gold quality
right coronary arteryUBERON:000162597.77gold quality
minor salivary glandUBERON:000183097.75gold quality
bone marrowUBERON:000237197.69gold quality
bone elementUBERON:000147497.68gold quality
muscle layer of sigmoid colonUBERON:003580597.68gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-ANND-3yes16.59
E-CURD-112yes15.37
E-MTAB-10042yes10.13
E-MTAB-7606no659.74
E-GEOD-70580no520.60
E-MTAB-5061no3.62

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, ATF6, ELF4, FOSL2, HIF1A, JUN, JUND, MYC, NFKB1, PARP1

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • localization to chromosome 11q12-13 in autosomal dominant osteopetrosis type I (PMID:12054167)
  • Sibling pair linkage and association studies between peak bone mineral density and the gene locus for the osteoclast-specific subunit (OC116) of the vacuolar proton pump on chromosome 11p12-13. (PMID:12161516)
  • Four novel single nucleotide mutations in the TCIRG1 gene encoding the 116-kDa osteoclast specific subunit of ATP6I affecting splice acceptor or donor sites result in aberrant transcription products. (PMID:12552563)
  • There is an association between a polymorphism affecting an API binding site in the promoter of the TCIRG1 gene and bone mass in Scottish women. (PMID:14523594)
  • 9 new TCIRG1 mutations were found in recessive osteopetrosis pts. 30% of the pts had c.1674-1G>A (aberrant splicing: r.1674_1884del) or c.2005C>T (protein variation: p.Arg669X). 40% were splicing regulatory sequence substitutions. (PMID:15300850)
  • we validated by RT-PCR six new alternative splice events in TCIRG1 in most of the 28 human tissues studied (PMID:15809087)
  • TIRC7 acts as an upstream regulatory molecule of cytotoxic T-lymphocyte antigen 4 (CTLA-4) expression. (PMID:17082597)
  • HLA-DR alpha 2 domain (sHLA-DRalpha2) induces negative signals by engaging TIRC7 on lymphocytes, inhibiting proliferation and inducing apoptosis in CD4+ and CD8+ T-cells via activation of the intrinsic pathway (PMID:18270567)
  • analysis of a novel Alu-Alu recombination-mediated genomic deletion in the TCIRG1 gene in five osteopetrotic patients (PMID:18715141)
  • Linkage disequilibrium (LD) mapping of the OPTB locus at the TCIRG1 region and found a unique splice site mutation c.807+5G>A in all Chuvashian OPTB patients studied. (PMID:19172990)
  • Mutations in TCIRG1, OSTM1, ClCN7, and TNFRSF11A genes were detected in nine, three, one, and one patientswith infantile malignant osteopetrosis, respectively. (PMID:19507210)
  • That the CLCN7 mutations provoke a phenotype as severe as the one caused by TCIRG1 loss of function suggests the affected residues to be crucial for the function of the ClC-7 chloride channel or chloride/proton-exchanger (PMID:20424301)
  • V-ATPase localization and activity in kidney cells is regulated via direct PKA-dependent phosphorylation of the A subunit at Ser-175 (PMID:20525692)
  • The novel mutation c.242delC of TCIRG1 in infantile malignant osteopetrosis (PMID:21042819)
  • Our data highlights the importance of two large genomic deletions and mutations in the 5’ UTR with respect to patient management and, more critically, to prenatal diagnosis (PMID:22231430)
  • The N termini of a-subunit isoforms are involved in signaling between vacuolar H+-ATPase (V-ATPase) and cytohesin-2 (PMID:23288846)
  • The function of vacuolar ATPase (V-ATPase) a subunit isoforms in invasiveness of MCF10a and MCF10CA1a human breast cancer cells. (PMID:24072707)
  • analysis demonstrates that CLCN7 and TCIRG1 mutations differentially affect bone matrix mineralization, and that there is a need to modify the current classification of osteopetrosis (PMID:24108692)
  • TIRC7 is involved in inflammation in multiple sclerosis and anti-TIRC7 mAb can prevent immune activation via selective inhibition of Th1- and Th17-associated cytokine expression. (PMID:24526664)
  • TIRC7 might be associated with the pathogenesis of ITP, and TIRC7 levels could be used as an indicator to evaluate patients’ response to HD-DXM treatment. (PMID:24617318)
  • TCIRG1-associated congenital neutropenia. (PMID:24753205)
  • Data indicate that the effects of epiregulin (EREG) and V-ATPase (TCIRG1) single nucleotide polymorphism (SNP) on pulmonary tuberculosis susceptibility, to the extent that they exist, are dependent on gene-gene interactions in West African populations. (PMID:24898387)
  • An A to T transversion in the fourth base of the intron 2 donor splice site (c.117+4A–>T) in TCIRG1 in the Ashkenazi Jewish (AJ) population was found to be responsible for osteopetrosis. (PMID:24989235)
  • Increased expression of TIRC7 in plasma was associated with the severity of acute graft-versus-host disease. (PMID:25623380)
  • an intronic region in TCIRG1 that seems to be particularly prone to splicing mutations, allowing the production of a small amount of protein sufficient to reduce the severity of the phenotype usually associated with TCIRG1 defects. (PMID:25829125)
  • TIRC7 might be involved in the pathogenesis of aplastic anemia. (PMID:26049920)
  • The highly invasive human breast cancer cell lines express higher levels of the a3 isoform than poorly invasive lines; knockdown of a3 reduces both expression of V-ATPases at the plasma membrane and in vitro invasion of breast tumor cells. (Review) (PMID:26906430)
  • In this study, whole exome sequencing (WES) was successfully used in six patients with malignant infantile osteopetrosis (MIOP) and identified mutations in four MIOP-related genes (CLCN7, TCIRG1, SNX10, and TNFRSF11A). (PMID:27187610)
  • Nine rare missense variants at evolutionarily conserved sites in TCIRG1 are associated with lower absolute neutrophil count. (PMID:27229898)
  • TCIRG1 gene mutation in a Chinese family is associated with infantile malignant osteopetrosis. (PMID:28604959)
  • The aim of this study was to develop a clinically applicable lentiviral vector expressing TCIRG1 to correct osteoclast function in Infantile malignant osteopetrosis (PMID:28726516)
  • TCIRG1 may be involved in endolysosomal transport-a process known to be important to development of early onset AD. (PMID:28738127)
  • Case Reports: TCIRG1-dependent osteopetrosis with a mild clinical course in Chinese patients. (PMID:28816234)
  • Since a3 subunit of V-ATPase complex plays a crucial role in bone resorption process, structurally abnormal a3 subunit might have adversely affected bone resorption process, leading to infantile osteopetrosis in Pakistani family. (PMID:29237407)
  • TCIRG1 functions as a metastasis-enhancing gene by modulating cellular growth and epithelial-mesenchymal transition in the hepatocellular carcinoma progression. (PMID:29303507)
  • TCIRG1 mutation is associated with osteopetrosis. (PMID:30431110)
  • mutations in SLC29A3 and TCIRG1 in patients with Sclerosing bone dysplasias with hallmarks of dysosteosclerosis. (PMID:30537558)
  • The study revealed that five of the twelve cases of autosomal recessive osteopetrosis carry at least one mutation of TCIRG1 gene. (PMID:30898715)
  • Novel c.G630A TCIRG1 mutation causes aberrant splicing resulting in an unusually mild form of autosomal recessive osteopetrosis. (PMID:31111556)
  • The Vacuolar H(+) ATPase alpha3 Subunit Negatively Regulates Migration and Invasion of Human Pancreatic Ductal Adenocarcinoma Cells. (PMID:32085585)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotcirg1aENSDARG00000016835
danio_reriotcirg1bENSDARG00000105142
mus_musculusTcirg1ENSMUSG00000001750
rattus_norvegicusTcirg1ENSRNOG00000017220
drosophila_melanogasterVha100-3FBGN0028669

Paralogs (3): ATP6V0A1 (ENSG00000033627), ATP6V0A4 (ENSG00000105929), ATP6V0A2 (ENSG00000185344)

Protein

Protein identifiers

V-type proton ATPase 116 kDa subunit a 3Q13488 (reviewed: Q13488)

Alternative names: Osteoclastic proton pump 116 kDa subunit, T-cell immune regulator 1, T-cell immune response cDNA7 protein, Vacuolar proton translocating ATPase 116 kDa subunit a isoform 3

All UniProt accessions (10): Q13488, A0A8V8TM28, A0A8V8TN16, A0A8V8TNB5, E9PM12, E9PMC5, E9PNA6, H0YCE3, H0YEL3, Q8TCH1

UniProt curated annotations — full annotation on UniProt →

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. V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment. Seems to be directly involved in T-cell activation.

Subunit / interactions. V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex. The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H. The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c’’, rotary subunit d, subunits e and f, and the accessory subunits ATP6AP1/Ac45 and ATP6AP2/PRR.

Subcellular location. Membrane.

Tissue specificity. Isoform long is highly expressed in osteoclastomas. Isoform short is highly expressed in thymus.

Disease relevance. Osteopetrosis, autosomal recessive 1 (OPTB1) [MIM:259700] A rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. Osteopetrosis occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Recessive osteopetrosis commonly manifests in early infancy with macrocephaly, feeding difficulties, evolving blindness and deafness, bone marrow failure, severe anemia, and hepatosplenomegaly. Deafness and blindness are generally thought to represent effects of pressure on nerves. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the V-ATPase 116 kDa subunit family.

Isoforms (2)

UniProt IDNamesCanonical?
Q13488-1Longyes
Q13488-2Short

RefSeq proteins (3): NP_001337988, NP_006010, NP_006044 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002490V-ATPase_116kDa_suFamily
IPR026028V-type_ATPase_116kDa_su_eukaFamily

Pfam: PF01496

UniProt features (31 total): topological domain 9, transmembrane region 8, sequence variant 8, region of interest 2, sequence conflict 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13488-F183.520.40

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-1222556ROS and RNS production in phagocytes
R-HSA-6798695Neutrophil degranulation
R-HSA-77387Insulin receptor recycling
R-HSA-917977Transferrin endocytosis and recycling
R-HSA-9639288Amino acids regulate mTORC1
R-HSA-983712Ion channel transport

MSigDB gene sets: 605 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, REACTOME_SIGNALING_BY_INSULIN_RECEPTOR, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, GOBP_VACUOLE_ORGANIZATION, GOBP_VESICLE_LOCALIZATION, GOBP_INFLAMMATORY_RESPONSE, GOBP_RESPONSE_TO_PEPTIDE, GOBP_B_CELL_ACTIVATION, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, ENK_UV_RESPONSE_KERATINOCYTE_UP, MODULE_45, GOBP_INSULIN_SECRETION, GOBP_T_CELL_HOMEOSTASIS

GO Biological Process (45): autophagosome assembly (GO:0000045), ossification (GO:0001503), osteoclast proliferation (GO:0002158), intracellular calcium ion homeostasis (GO:0006874), apoptotic process (GO:0006915), inflammatory response (GO:0006954), cellular defense response (GO:0006968), vacuolar acidification (GO:0007035), protein catabolic process in the vacuole (GO:0007039), lysosomal lumen acidification (GO:0007042), positive regulation of cell population proliferation (GO:0008284), regulation of proton transport (GO:0010155), response to silver ion (GO:0010272), gene expression (GO:0010467), regulation of gene expression (GO:0010468), immunoglobulin mediated immune response (GO:0016064), macroautophagy (GO:0016236), optic nerve development (GO:0021554), establishment of cell polarity (GO:0030010), B cell differentiation (GO:0030183), T cell differentiation (GO:0030217), osteoclast differentiation (GO:0030316), ruffle organization (GO:0031529), memory T cell activation (GO:0035709), T-helper 1 cell activation (GO:0035711), T cell homeostasis (GO:0043029), tooth eruption (GO:0044691), bone resorption (GO:0045453), regulation of osteoblast differentiation (GO:0045667), pH reduction (GO:0045851), regulation of insulin secretion (GO:0050796), establishment of vesicle localization (GO:0051650), retina development in camera-type eye (GO:0060041), hematopoietic stem cell homeostasis (GO:0061484), enamel mineralization (GO:0070166), cellular response to cytokine stimulus (GO:0071345), phagosome acidification (GO:0090383), dentin mineralization (GO:0097188), proton transmembrane transport (GO:1902600), monoatomic ion transport (GO:0006811)

GO Molecular Function (3): proton-transporting ATPase activity, rotational mechanism (GO:0046961), ATPase binding (GO:0051117), protein binding (GO:0005515)

GO Cellular Component (16): vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220), nucleus (GO:0005634), lysosomal membrane (GO:0005765), late endosome (GO:0005770), plasma membrane (GO:0005886), endosome membrane (GO:0010008), apical plasma membrane (GO:0016324), vacuolar proton-transporting V-type ATPase complex (GO:0016471), phagocytic vesicle membrane (GO:0030670), proton-transporting V-type ATPase complex (GO:0033176), ficolin-1-rich granule membrane (GO:0101003), lysosome (GO:0005764), membrane (GO:0016020), secretory granule membrane (GO:0030667), proton-transporting V-type ATPase, V0 domain (GO:0033179), phagocytic vesicle (GO:0045335)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Innate Immune System2
Signaling by Insulin receptor1
Iron uptake and transport1
Cellular response to starvation1
Transport of small molecules1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
defense response2
vacuolar membrane2
endosome2
cytoplasmic vesicle membrane2
bounding membrane of organelle2
proton-transporting V-type ATPase complex2
Atg12 activating enzyme activity1
protein-phosphatidylethanolamide deconjugating activity1
Atg12 conjugating enzyme activity1
Atg12 ligase activity1
organelle assembly1
Atg1/ULK1 kinase complex assembly1
autophagosome organization1
multicellular organismal process1
leukocyte proliferation1
intracellular monoatomic cation homeostasis1
calcium ion homeostasis1
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
intracellular pH reduction1
vacuole1
protein catabolic process1
vacuolar acidification1
cell population proliferation1
regulation of cell population proliferation1
positive regulation of cellular process1
proton transmembrane transport1
regulation of monoatomic cation transmembrane transport1
response to metal ion1
macromolecule biosynthetic process1
gene expression1
regulation of macromolecule biosynthetic process1
B cell mediated immunity1
autophagosome assembly1
autophagy1
cranial nerve development1
establishment or maintenance of cell polarity1
lymphocyte differentiation1
B cell activation1

Protein interactions and networks

STRING

1788 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TCIRG1ATP6V1B1P15313979
TCIRG1CLCN7P51798965
TCIRG1OSTM1Q86WC4964
TCIRG1ATP12AP54707923
TCIRG1ATP4AP20648923
TCIRG1PLEKHM1Q9Y4G2889
TCIRG1CA2P00918869
TCIRG1CCKBRP32239817
TCIRG1ATP6V1B2P21281797
TCIRG1ATP6V0CP27449792
TCIRG1ATP6V0D2Q8N8Y2792
TCIRG1ATP6V1C1P21283782
TCIRG1ATP6V0D1P12953779
TCIRG1ATP6V1AP38606773
TCIRG1ATP6V1C2Q8NEY4773

IntAct

52 interactions, top by confidence:

ABTypeScore
ATP6AP2ATP6V0Cpsi-mi:“MI:0914”(association)0.730
TCIRG1ATP6AP2psi-mi:“MI:0914”(association)0.640
ATP6V1C2ATP6V1G1psi-mi:“MI:0914”(association)0.640
TLX3TCIRG1psi-mi:“MI:0915”(physical association)0.560
POGZTCIRG1psi-mi:“MI:0915”(physical association)0.560
ADD2ADD1psi-mi:“MI:0914”(association)0.560
ATP6AP2ATP6V1C1psi-mi:“MI:0914”(association)0.530
TCIRG1AP3D1psi-mi:“MI:0914”(association)0.530
ATP6V1G2ATP6V1B1psi-mi:“MI:0914”(association)0.530
GORASP1PPP6R2psi-mi:“MI:0914”(association)0.530
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
MCAMLGALS8psi-mi:“MI:0914”(association)0.530
RFFLTUSC2psi-mi:“MI:0914”(association)0.530
pipB2SCDpsi-mi:“MI:0914”(association)0.460
PLEKHN1TCIRG1psi-mi:“MI:0915”(physical association)0.400
GPC1SNAP23psi-mi:“MI:0915”(physical association)0.400
GPC1GANABpsi-mi:“MI:0915”(physical association)0.400
SDC1ILVBLpsi-mi:“MI:0915”(physical association)0.400
TCIRG1KCNK1psi-mi:“MI:0915”(physical association)0.370
TCIRG1TERF1psi-mi:“MI:0915”(physical association)0.370
SYNCRIPARHGAP32psi-mi:“MI:0914”(association)0.350
BAG6CNOT1psi-mi:“MI:0914”(association)0.350
SORT1SH3PXD2Bpsi-mi:“MI:0914”(association)0.350
GOLT1Bpsi-mi:“MI:0914”(association)0.350
ATP6V0D1psi-mi:“MI:0914”(association)0.350
ATP6V0D2ATP6V0Cpsi-mi:“MI:0914”(association)0.350
NS3C15orf61psi-mi:“MI:0914”(association)0.350
TMEM223psi-mi:“MI:0914”(association)0.350

BioGRID (91): TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Reconstituted Complex), TCIRG1 (Protein-RNA), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), TCIRG1 (Affinity Capture-MS), POGZ (Two-hybrid)

ESM2 similar proteins: A4FUB8, E9QBI7, O35394, O95070, O97681, P15920, P58872, P58873, Q0DWA9, Q0P5E4, Q12270, Q12893, Q13488, Q1RMH4, Q28C60, Q3UVK0, Q4V8F3, Q52NJ0, Q5RBS4, Q5XIT3, Q5Z413, Q6BSA9, Q6C741, Q6CDV6, Q6CR06, Q6DCK1, Q6FSG0, Q6P6G5, Q6UPR8, Q755H8, Q7Z2K6, Q874X5, Q8BHC7, Q8BXJ9, Q8RXQ2, Q8TEB9, Q8VC82, Q8VZ96, Q91VU1, Q91XB7

Diamond homologs: A1A5G6, B2MZD0, G5EEK9, G5EGP4, O13742, O29106, O57721, O97681, P15920, P25286, P30628, P32563, P37296, Q01290, Q13488, Q29466, Q54E04, Q57675, Q5JDS2, Q5R422, Q8AVM5, Q8RWZ7, Q8W4S4, Q920R6, Q93050, Q9HBG4, Q9I8D0, Q9SJT7, Q9UWW3, Q9UXU2, Q9Y487, Q9Z1G4, Q9YEA0, O27041, O83544, Q9RWH3, Q9HND8

SIGNOR signaling

1 interactions.

AEffectBMechanism
TCIRG1“form complex”V-ATPasebinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy568.5×4e-07
Insulin receptor recycling862.1×6e-11
Transferrin endocytosis and recycling860.1×6e-11
ROS and RNS production in phagocytes854.8×9e-11
Amino acids regulate mTORC1832.7×6e-09
Ion channel transport815.7×2e-06

GO biological processes:

GO termPartnersFoldFDR
synaptic vesicle lumen acidification7102.4×1e-10
vacuolar acidification557.2×4e-06
regulation of macroautophagy837.0×1e-08
proton transmembrane transport524.4×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

1777 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic103
Likely pathogenic115
Uncertain significance614
Likely benign765
Benign26

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1068788NM_006019.4(TCIRG1):c.797del (p.Glu266fs)Pathogenic
1069133NM_006019.4(TCIRG1):c.685G>T (p.Gly229Ter)Pathogenic
1070235NM_006019.4(TCIRG1):c.2233dup (p.Ala745fs)Pathogenic
1074841NM_006019.4(TCIRG1):c.524_527dup (p.His177fs)Pathogenic
1075445NM_006019.4(TCIRG1):c.1349dup (p.Met450fs)Pathogenic
1362729NM_006019.4(TCIRG1):c.480del (p.Pro161fs)Pathogenic
1388769NM_006019.4(TCIRG1):c.1498del (p.Leu500fs)Pathogenic
1418205NM_006019.4(TCIRG1):c.1776G>A (p.Trp592Ter)Pathogenic
1439125NM_006019.4(TCIRG1):c.904_952del (p.Val302fs)Pathogenic
1447238NM_006019.4(TCIRG1):c.2383_2384del (p.Ala796fs)Pathogenic
1447247NM_006019.4(TCIRG1):c.2160_2178del (p.Ile721fs)Pathogenic
1449740NC_000011.9:g.(?67814890)(67815449_?)delPathogenic
1451544NM_006019.4(TCIRG1):c.1736del (p.Gly579fs)Pathogenic
1452936NM_006019.4(TCIRG1):c.1230del (p.Leu411fs)Pathogenic
1453401NM_006019.4(TCIRG1):c.474dup (p.Gly159fs)Pathogenic
1453967NM_006019.4(TCIRG1):c.2331dup (p.Ala778fs)Pathogenic
1455306NC_000011.9:g.(?67814890)(67818296_?)delPathogenic
1457984NM_006019.4(TCIRG1):c.174_175del (p.Cys58_Glu59delinsTer)Pathogenic
1458624NM_006019.4(TCIRG1):c.1348_1376dup (p.Phe459fs)Pathogenic
1460225NM_006019.4(TCIRG1):c.688C>T (p.Gln230Ter)Pathogenic
1492118NM_006019.4(TCIRG1):c.1305+1G>APathogenic
1684665NM_006019.4(TCIRG1):c.807+2T>GPathogenic
1684673NM_006019.4(TCIRG1):c.969G>A (p.Trp323Ter)Pathogenic
1684679NM_006019.4(TCIRG1):c.2236+1G>CPathogenic
1684680NM_006019.4(TCIRG1):c.1885C>T (p.Gln629Ter)Pathogenic
189246NM_006019.4(TCIRG1):c.1674-1G>APathogenic
1913378NM_006019.4(TCIRG1):c.1370_1384del (p.Thr457_Tyr461del)Pathogenic
1980632NM_006019.4(TCIRG1):c.1037_1040dup (p.Val348fs)Pathogenic
1988317NM_006019.4(TCIRG1):c.1560G>A (p.Trp520Ter)Pathogenic
2008908NM_006019.4(TCIRG1):c.2104_2105del (p.Glu702fs)Pathogenic

SpliceAI

4169 predictions. Top by Δscore:

VariantEffectΔscore
11:68039117:GGG:Gdonor_gain1.0000
11:68039118:GG:Gdonor_gain1.0000
11:68039118:GGG:Gdonor_gain1.0000
11:68039119:GG:Gdonor_gain1.0000
11:68039120:G:GGdonor_gain1.0000
11:68039120:GTGA:Gdonor_loss1.0000
11:68041261:C:Gacceptor_gain1.0000
11:68041263:CACA:Cacceptor_loss1.0000
11:68041264:ACAG:Aacceptor_gain1.0000
11:68041266:A:AGacceptor_gain1.0000
11:68041266:AG:Aacceptor_gain1.0000
11:68041267:G:GTacceptor_gain1.0000
11:68041267:GG:Gacceptor_gain1.0000
11:68041267:GGA:Gacceptor_gain1.0000
11:68041267:GGAC:Gacceptor_gain1.0000
11:68041267:GGACC:Gacceptor_gain1.0000
11:68041345:GC:Gdonor_gain1.0000
11:68041384:GAGAC:Gdonor_gain1.0000
11:68041386:GAC:Gdonor_gain1.0000
11:68041387:ACG:Adonor_loss1.0000
11:68041389:G:GGdonor_gain1.0000
11:68041747:CCACA:Cacceptor_loss1.0000
11:68041748:CACA:Cacceptor_loss1.0000
11:68041749:ACAG:Aacceptor_loss1.0000
11:68041750:CA:Cacceptor_loss1.0000
11:68041751:A:ACacceptor_loss1.0000
11:68041751:A:AGacceptor_gain1.0000
11:68041752:G:GAacceptor_gain1.0000
11:68041752:GCTC:Gacceptor_gain1.0000
11:68041752:GCTCA:Gacceptor_gain1.0000

AlphaMissense

5384 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:68050222:T:CL735P0.999
11:68050230:T:AW738R0.999
11:68050230:T:CW738R0.999
11:68048926:G:CK534N0.998
11:68048926:G:TK534N0.998
11:68050232:G:CW738C0.997
11:68050232:G:TW738C0.997
11:68050239:A:CS741R0.997
11:68050241:C:AS741R0.997
11:68050241:C:GS741R0.997
11:68050658:T:CL803P0.997
11:68050748:T:CF808L0.997
11:68050750:C:AF808L0.997
11:68050750:C:GF808L0.997
11:68050760:T:CF812L0.997
11:68050762:C:AF812L0.997
11:68050762:C:GF812L0.997
11:68047477:T:CF404L0.996
11:68047479:C:AF404L0.996
11:68047479:C:GF404L0.996
11:68048917:C:AN531K0.996
11:68048917:C:GN531K0.996
11:68050213:C:AA732D0.996
11:68050645:C:GH799D0.996
11:68050185:T:CF723L0.995
11:68050187:C:AF723L0.995
11:68050187:C:GF723L0.995
11:68050204:C:AS729Y0.995
11:68050204:C:TS729F0.995
11:68050216:C:TS733F0.995

dbSNP variants (sampled 300 via entrez): RS1000047233 (11:68037381 G>A,T), RS1000520573 (11:68051772 G>A,C), RS1000538925 (11:68043362 G>A), RS1000613230 (11:68044401 G>A), RS1000664757 (11:68048025 G>C), RS1000666892 (11:68047264 C>A,G,T), RS1000724351 (11:68048199 T>C), RS1000940711 (11:68037432 T>A,C), RS1001080626 (11:68037629 C>G), RS1001191391 (11:68038976 T>A,C), RS1001228717 (11:68043137 A>AG), RS1001671587 (11:68044470 G>C), RS1001985320 (11:68047771 G>A), RS1002118866 (11:68038095 C>T), RS1002149192 (11:68038508 G>A,C)

Disease associations

OMIM: gene MIM:604592 | disease phenotypes: MIM:259700, MIM:202700, MIM:224300, MIM:200150, MIM:618222

GenCC curated gene-disease

DiseaseClassificationInheritance
autosomal recessive osteopetrosis 1DefinitiveAutosomal recessive
autosomal recessive osteopetrosisDefinitiveAutosomal recessive
dysosteosclerosisSupportiveAutosomal recessive
autosomal recessive osteopetrosis 6SupportiveAutosomal recessive
autosomal dominant severe congenital neutropeniaSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
autosomal recessive osteopetrosis 1DefinitiveAR
dysosteosclerosisLimitedAR

Mondo (11): autosomal recessive osteopetrosis 1 (MONDO:0009815), osteopetrosis (MONDO:0017198), neutropenia, severe congenital, 1, autosomal dominant (MONDO:0042490), bone disorder (MONDO:0005381), neutropenia (MONDO:0001475), dysosteosclerosis (MONDO:0009138), autosomal recessive osteopetrosis (MONDO:0019026), VPS13A-related neurodegenerative disease (MONDO:0008695), mitochondrial complex I deficiency, nuclear type 2 (MONDO:0032606), autosomal recessive osteopetrosis 6 (MONDO:0012679), autosomal dominant severe congenital neutropenia (MONDO:0008742)

Orphanet (5): Autosomal recessive malignant osteopetrosis (Orphanet:667), Osteopetrosis and related disorders (Orphanet:2781), Rare bone disease related to a common gene or pathway defect (Orphanet:364803), Dysosteosclerosis (Orphanet:1782), Choreoacanthocytosis (Orphanet:2388)

HPO phenotypes

127 total (30 of 127 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000155Oral ulcer
HP:0000164Abnormality of the dentition
HP:0000230Gingivitis
HP:0000238Hydrocephalus
HP:0000256Macrocephaly
HP:0000316Hypertelorism
HP:0000365Hearing impairment
HP:0000388Otitis media
HP:0000505Visual impairment
HP:0000597Ophthalmoparesis
HP:0000618Blindness
HP:0000639Nystagmus
HP:0000648Optic atrophy
HP:0000649Abnormality of visual evoked potentials
HP:0000670Carious teeth
HP:0000682Abnormal dental enamel morphology
HP:0000684Delayed eruption of teeth
HP:0000689Dental malocclusion
HP:0000704Periodontitis
HP:0000707Abnormality of the nervous system
HP:0000772Abnormal rib morphology
HP:0000774Narrow chest
HP:0000926Platyspondyly
HP:0000938Osteopenia
HP:0000944Abnormal metaphysis morphology
HP:0000978Bruising susceptibility
HP:0000980Pallor
HP:0001028Hemangioma
HP:0001249Intellectual disability

GWAS associations

3 associations (top):

StudyTraitp-value
GCST006979_403Heel bone mineral density2.000000e-12
GCST006979_404Heel bone mineral density7.000000e-11
GCST90002405_285Reticulocyte count3.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0009270heel bone mineral density
EFO:0007986reticulocyte count

MeSH disease descriptors (7)

DescriptorNameTree numbers
D001847Bone DiseasesC05.116
D009503NeutropeniaC15.378.243.750.184.564; C15.378.553.546.184.564
D010022OsteopetrosisC05.116.099.708.702.678
C562973Dysosteosclerosis (supp.)
C565969Neutropenia, Severe Congenital, Autosomal Dominant 1 (supp.)
C564915Osteopetrosis, Autosomal Recessive 1 (supp.)
C566931Osteopetrosis, Autosomal Recessive 6 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — V-type ATPase

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases expression, increases methylation4
Air Pollutantsincreases abundance, decreases expression, affects expression3
Particulate Matterdecreases expression, increases abundance, affects cotreatment, increases expression3
Nickelincreases expression2
Rotenoneincreases expression2
Smokedecreases expression, increases abundance2
Tobacco Smoke Pollutionaffects expression, decreases expression2
Tretinoinincreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
beta-lapachonedecreases expression, increases expression1
sodium arseniteincreases expression1
perfluorooctanoic aciddecreases expression1
manganese chlorideincreases abundance, increases expression1
tamibaroteneincreases expression1
entinostatincreases expression, affects cotreatment1
pinostrobinincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
MT19c compounddecreases expression1
Temozolomidedecreases expression1
Ethanolaffects cotreatment, increases abundance, increases expression1
Arsenicaffects methylation1
Aspirinincreases expression1
Vehicle Emissionsdecreases expression, increases abundance1
Cisplatinaffects cotreatment, increases expression1
Demecolcinedecreases expression1

Cellosaurus cell lines

4 cell lines: 4 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D0M3SYSUSCi004-AInduced pluripotent stem cellMale
CVCL_YB57UNIBSi010-AInduced pluripotent stem cellMale
CVCL_YB58UNIBSi010-BInduced pluripotent stem cellMale
CVCL_YB59UNIBSi010-CInduced pluripotent stem cellMale

Clinical trials (associated diseases)

199 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00030758PHASE4UNKNOWNFilgrastim or Pegfilgrastim in Preventing Neutropenia in Women Receiving Chemotherapy Following Surgery for Breast Cancer
NCT00125723PHASE4COMPLETEDFIRST - Study of Pegfilgrastim Administered in the First and Subsequent Cycles of Myelosuppressive Chemotherapy
NCT00194857PHASE4TERMINATEDTreatment of Anemia and Neutropenia in HIV/HCV Coinfected Patients Treated With Pegylated Interferon and Ribavirin
NCT00257790PHASE4COMPLETEDThe Tobramycin Study
NCT00277160PHASE4COMPLETEDA Study of Primary Prophylaxis With Neulasta (Pegfilgrastim) Versus Secondary Prophylaxis After Chemotherapy in Elderly Subjects (>/= 65 Years Old) With Cancer
NCT00686543PHASE4COMPLETEDOral Posaconazole in High Risk Patients With Gastrointestinal Dysfunction (Study P05115)
NCT01086878PHASE4COMPLETEDSafety of Cotrimoxazole in HIV- and HAART-exposed Infants
NCT01114165PHASE4COMPLETEDValue of the LightCycler® SeptiFast Test MGRADE for the Pathogen Detection in Neutropenic Hematological Patients
NCT01135589PHASE4UNKNOWNMicafungin Prevention Study for Fungal Disease in Child Receiving Allogenic Hematopoietic Stem Cell Transplantation
NCT01571518PHASE4UNKNOWNPrevention of Neutropenia After Using G-CSF With TAC Chemotherapy
NCT02621905PHASE4COMPLETEDSteady-State Comparative Bioavailability Study in Prophylaxis Patients of Lozanoc® 50 mg With Sporanox® 100 mg
NCT02967341PHASE4UNKNOWNBlood Draw Validation for Ciprofloxacin Pharmacokinetic Research in Pediatric Cancer Patients
NCT04009941PHASE4COMPLETEDEfficacy and Safety of 4.5mg PEG-rhG-CSF Per Cycle in Preventing Neutropenia After Intensive Chemotherapy for Breast Cancer
NCT04904614PHASE4COMPLETEDLetermovir Use in Heart Transplant Recipients
NCT05626530PHASE4RECRUITINGLetermovir for Secondary Prophylaxis in Solid Organ Transplant Recipients
NCT06145321PHASE4ACTIVE_NOT_RECRUITINGContinuous Versus Bolus Administration of G-CSF in Children With Cancer
NCT00004402PHASE3COMPLETEDPhase III Randomized Study of Interferon Gamma in Children With Severe, Congenital Osteopetrosis
NCT00001338PHASE3COMPLETEDA Prospective, Randomized, Phase III Trial of FLAC (5-Fluorouracil, Leucovorin, Adriamycin, Cytoxan) Chemotherapy With GM-CSF (Granulocyte-Macrophage Colony-Stimulating Factor) Versus PIXY 321 in Advanced Breast Cancer
NCT00001646PHASE3COMPLETEDVoriconazole vs. Amphotericin B in the Treatment of Invasive Aspergillosis
NCT00002658PHASE3UNKNOWNCombination Chemotherapy, Biological Therapy, and Bone Marrow Transplantation in Treating Patients With Acute Myeloid Leukemia
NCT00002719PHASE3COMPLETEDCombination Chemotherapy With or Without G-CSF in Treating Older Patients With Acute Myeloid Leukemia
NCT00003739PHASE3COMPLETEDAntibiotic Therapy With or Without G-CSF in Treating Children With Neutropenia and Fever Caused by Chemotherapy
NCT00020865PHASE3UNKNOWNLevofloxacin Compared With Cefepime in Treating Cancer Patients With Fever and Neutropenia
NCT00035594PHASE3COMPLETEDPegfilgrastim as Support to Advanced Breast Cancer Patients Receiving Chemotherapy
NCT00044486PHASE3COMPLETEDProphylaxis Trial of Posaconazole Versus Standard Azole Therapy for Neutropenic Patients (Study P01899)
NCT00107081PHASE3TERMINATEDLow-risk Fever and Neutropenia in Children With Cancer: Safety and Efficacy of Oral Antibiotics in an Outpatient Setting
NCT00445497PHASE3UNKNOWNEarly Hospital Discharge or Standard Inpatient Care in Cancer Patients Receiving Antibiotics for Febrile Neutropenia
NCT00529282PHASE3TERMINATEDA Study of Ceftobiprole in Patients With Fever and Neutropenia.
NCT00627393PHASE3COMPLETEDSafety and Effectiveness of Granulocyte Transfusions in Resolving Infection in People With Neutropenia (The RING Study)
NCT00770172PHASE3COMPLETEDG-CSF in Preventing Neutropenia in Patients With Solid Tumors Who Are Receiving Chemotherapy
NCT00784368PHASE3COMPLETEDA Pharmacokinetic Study of JK1211(Itraconazole [Itrizole]) Oral Solution in Participants With Deep Mycosis and Those With Febrile Neutropenia Suspected of Fungal Infection
NCT00806351PHASE3TERMINATEDAn Evaluation Of The Effectiveness And Safety Of Anidulafungin Compared To Caspofungin For The Treatment Of Serious Fungal Infection Due To Candida In Patients With A Dysfunctional Immune System
NCT00911170PHASE3COMPLETEDPAVES: Pegfilgrastim Anti-vascular Endothelial Growth Factor (VEGF) Evaluation Study
NCT01307579PHASE3COMPLETEDCaspofungin Versus Fluconazole in Preventing Invasive Fungal Infections (IFI) in Patients Undergoing Chemotherapy for Acute Myeloid Leukemia
NCT01371656PHASE3COMPLETEDLevofloxacin in Preventing Infection in Young Patients With Acute Leukemia Receiving Chemotherapy or Undergoing Stem Cell Transplantation
NCT01560195PHASE3UNKNOWNA Study of Pegylated rhG-CSF as Support to Advanced Non-Small-Cell Lung Cancer (NSCLC) Patients Receiving Chemotherapy Receiving Chemotherapy
NCT01611051PHASE3COMPLETEDA Study Comparing Pegylated rhG-CSF and rhG-CSF as Support to Breast Cancer Patients Receiving Chemotherapy
NCT02238873PHASE3UNKNOWNPegfilgrastim on Day +3 Compared to Day +1 After Salvage Chemotherapy for Patients With Refractory or Relapsed Aggressive Lymphoma
NCT02414581PHASE3COMPLETEDMouthwash With Chlorhexidine 0.12%/Ethyl Alcohol 7% Compared to Ethyl Alcohol 7%
NCT02643420PHASE3COMPLETEDSPI-2012 vs Pegfilgrastim in the Management of Neutropenia in Participants With Breast Cancer With Docetaxel and Cyclophosphamide (ADVANCE)