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ITPKB

gene
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Also known as IP3KBIP3-3KB

Summary

ITPKB (inositol-trisphosphate 3-kinase B, HGNC:6179) is a protein-coding gene on chromosome 1q42.12, encoding Inositol-trisphosphate 3-kinase B (P27987). Catalyzes the phosphorylation of 1D-myo-inositol 1,4,5-trisphosphate (InsP3) into 1D-myo-inositol 1,3,4,5-tetrakisphosphate and participates to the regulation of calcium homeostasis.

The protein encoded by this protein regulates inositol phosphate metabolism by phosphorylation of second messenger inositol 1,4,5-trisphosphate to Ins(1,3,4,5)P4. The activity of this encoded protein is responsible for regulating the levels of a large number of inositol polyphosphates that are important in cellular signaling. Both calcium/calmodulin and protein phosphorylation mechanisms control its activity.

Source: NCBI Gene 3707 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): ITPKB deficiency (Limited, ClinGen) — +2 more curated relationships
  • GWAS associations: 13
  • Clinical variants (ClinVar): 159 total
  • Expression (HPA): Tissue enhanced — highest in area postrema, posterior thalamic nucleus, globus pallidus, externus
  • GTEx eGene: eQTL in 15 tissues, sQTL in 3 (q < 0.05)
  • Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.34 (highly constrained)
  • MANE Select transcript: NM_002221
  • Notable: 159 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6179
Approved symbolITPKB
Nameinositol-trisphosphate 3-kinase B
Location1q42.12
Locus typegene with protein product
StatusApproved
AliasesIP3KB, IP3-3KB
Ensembl geneENSG00000143772
Ensembl biotypeprotein_coding
OMIM147522
Entrez3707

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

MANE Select: ENST00000429204

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 5: 1

ENST00000429204, ENST00000272117, ENST00000366784, ENST00000926664, ENST00001112273, ENST00001112274, ENST00001145801

RefSeq mRNA: 2 — MANE Select: NM_002221 NM_001388404, NM_002221

CCDS: CCDS1555, CCDS91167

Canonical transcript exons

ENST00000429204 — 8 exons

ExonStartEnd
ENSE00000961885226648672226648771
ENSE00000961886226647167226647380
ENSE00000961887226641921226642125
ENSE00000961888226639557226639658
ENSE00000961889226637679226637750
ENSE00001145367226631690226634886
ENSE00001442611226735527226737663
ENSE00001658024226739041226739282

Expression profiles

Bgee: expression breadth ubiquitous, 268 present calls, max score 99.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.3494 / max 846.7999, expressed in 1678 samples.

Highest expression (Bgee): lateral globus pallidus, substantia nigra pars reticulata, globus pallidus, dorsal motor nucleus of vagus nerve, medial globus pallidus.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ITPKB is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 15 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

18 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Whole Bloodeqtl2.1e-07-0.101:226739756:G:A
Muscle Skeletalsqtl2.4e-05+0.751:226044737:C:T
Skin Sun Exposed Lower legeqtl6.1e-05-0.211:226632551:C:G
Skin Not Sun Exposed Suprapubiceqtl1.4e-04-0.211:226638745:G:A
Colon Sigmoideqtl1.9e-03-0.221:226667855:C:T
Nerve Tibialeqtl3.9e-03+0.111:226658690:C:A
Lungeqtl4.3e-03-0.131:226744910:A:G
Artery Aortaeqtl6.4e-03+0.171:226787569:A:G
Adrenal Glandeqtl8.3e-03-1.211:226788031:A:C
Brain Nucleus accumbens basal gangliaeqtl1.4e-02-0.451:227738515:C:T
Artery Tibialeqtl1.6e-02+0.301:227430547:G:A
Brain Frontal Cortex BA9eqtl2.6e-02+0.351:227702338:C:T
Cells Cultured fibroblastseqtl3.1e-02-0.391:226890808:T:G
Muscle Skeletaleqtl3.2e-02+0.231:227301521:A:G
Pancreassqtl3.6e-02-1.661:227518345:G:C
Heart Left Ventricleeqtl3.7e-02-0.121:225743354:G:A
Esophagus Mucosasqtl3.9e-02+1.091:226538365:G:A
Stomacheqtl4.4e-02-0.141:226695585:G:A

FANTOM5 promoters

8 alternative TSS:

Promoter IDTPM avgSamples expressed
1778129.22211615
177823.22811209
177770.2833112
177780.250073
177800.2187107
177750.053834
177790.052134
177760.041323

Top tissues by expression

showing 100 of 291 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lateral globus pallidusUBERON:000247699.09gold quality
substantia nigra pars reticulataUBERON:000196698.06gold quality
globus pallidusUBERON:000187597.70gold quality
dorsal motor nucleus of vagus nerveUBERON:000287097.60gold quality
medial globus pallidusUBERON:000247797.42gold quality
inferior olivary complexUBERON:000212797.38gold quality
substantia nigra pars compactaUBERON:000196597.34gold quality
subthalamic nucleusUBERON:000190697.24gold quality
ventral tegmental areaUBERON:000269197.07gold quality
medulla oblongataUBERON:000189697.01gold quality
superior vestibular nucleusUBERON:000722796.95gold quality
middle frontal gyrusUBERON:000270296.84gold quality
inferior vagus X ganglionUBERON:000536396.78gold quality
midbrainUBERON:000189196.51gold quality
substantia nigraUBERON:000203896.48gold quality
dorsal plus ventral thalamusUBERON:000189796.29gold quality
lateral nuclear group of thalamusUBERON:000273695.73gold quality
cranial nerve IIUBERON:000094195.71gold quality
spinal cordUBERON:000224095.17gold quality
C1 segment of cervical spinal cordUBERON:000646995.13gold quality
amygdalaUBERON:000187694.90gold quality
ponsUBERON:000098894.49gold quality
putamenUBERON:000187494.30gold quality
hypothalamusUBERON:000189894.27gold quality
lower esophagus muscularis layerUBERON:003583393.60gold quality
caudate nucleusUBERON:000187393.59gold quality
lower esophagusUBERON:001347393.56gold quality
CA1 field of hippocampusUBERON:000388193.46gold quality
thymusUBERON:000237093.21gold quality
temporal lobeUBERON:000187192.98gold quality
nucleus accumbensUBERON:000188292.98gold quality
sural nerveUBERON:001548892.88gold quality
Ammon’s hornUBERON:000195492.67gold quality
body of uterusUBERON:000985392.63gold quality
esophagogastric junction muscularis propriaUBERON:003584192.18gold quality
corpus callosumUBERON:000233692.01gold quality
muscle layer of sigmoid colonUBERON:003580591.53gold quality
olfactory bulbUBERON:000226491.51gold quality
myometriumUBERON:000129691.47gold quality
postcentral gyrusUBERON:000258191.44gold quality
parietal lobeUBERON:000187291.20gold quality
left uterine tubeUBERON:000130391.11gold quality
paraflocculusUBERON:000535191.08gold quality
entorhinal cortexUBERON:000272891.04gold quality
right frontal lobeUBERON:000281090.71gold quality
Brodmann (1909) area 9UBERON:001354090.16gold quality
telencephalonUBERON:000189390.11gold quality
mucosa of stomachUBERON:000119990.09gold quality
trigeminal ganglionUBERON:000167590.00gold quality
cingulate cortexUBERON:000302789.95gold quality
smooth muscle tissueUBERON:000113589.94gold quality
apex of heartUBERON:000209889.94gold quality
anterior cingulate cortexUBERON:000983589.90gold quality
pigmented layer of retinaUBERON:000178289.79gold quality
retinaUBERON:000096689.77gold quality
bloodUBERON:000017889.69gold quality
granulocyteCL:000009489.65gold quality
lymph nodeUBERON:000002988.94gold quality
endocervixUBERON:000045888.90gold quality
forebrainUBERON:000189088.87gold quality
central nervous systemUBERON:000101788.68gold quality
colonic epitheliumUBERON:000039788.61gold quality
parotid glandUBERON:000183188.48gold quality
brainUBERON:000095588.47gold quality
corpus epididymisUBERON:000435988.43gold quality
cerebral cortexUBERON:000095688.25gold quality
choroid plexus epitheliumUBERON:000391188.15gold quality
lower lobe of lungUBERON:000894988.07gold quality
frontal cortexUBERON:000187088.01gold quality
frontal lobeUBERON:001652588.00gold quality
dorsolateral prefrontal cortexUBERON:000983487.85gold quality
neocortexUBERON:000195087.74gold quality
superior frontal gyrusUBERON:000266187.66gold quality
ectocervixUBERON:001224987.41gold quality
peripheral nervous systemUBERON:000001087.03gold quality
tibial nerveUBERON:000132387.03gold quality
cauda epididymisUBERON:000436086.92gold quality
prefrontal cortexUBERON:000045186.49gold quality
esophagusUBERON:000104386.41gold quality
sigmoid colonUBERON:000115986.28gold quality
right lungUBERON:000216786.14gold quality
urinary bladderUBERON:000125586.12gold quality
adult organismUBERON:000702386.00gold quality
Brodmann (1909) area 46UBERON:000648385.95gold quality
fundus of stomachUBERON:000116085.94gold quality
adipose tissue of abdominal regionUBERON:000780885.83gold quality
omental fat padUBERON:001041485.83gold quality
peritoneumUBERON:000235885.81gold quality
occipital lobeUBERON:000202185.76gold quality
spleenUBERON:000210685.59gold quality
deciduaUBERON:000245085.55gold quality
Brodmann (1909) area 10UBERON:001354185.52gold quality
subcutaneous adipose tissueUBERON:000219085.29gold quality
vermiform appendixUBERON:000115485.10gold quality
upper arm skinUBERON:000426384.97gold quality
adipose tissueUBERON:000101384.92gold quality
skin of legUBERON:000151184.86gold quality
dorsal root ganglionUBERON:000004484.81gold quality
prostate glandUBERON:000236784.72gold quality
connective tissueUBERON:000238484.66gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-GEOD-81383yes256.42
E-CURD-119yes49.78
E-HCAD-35yes23.35
E-HCAD-25yes21.66
E-ANND-3yes8.30
E-MTAB-6058no14.64

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 76 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Choroid plexustissue197.2
Hippocampustissue164.0medium
Locus coeruleustissue158.3
Nucleus accumbenstissue136.5
Postcentral gyrustissue109.7
Spinal cordtissue67.2
Periaqueductal graytissue60.3
Midbraintissue59.5
Medulla oblongatatissue59.3
Substantia nigratissue51.0
Ponstissue49.6
Thalamustissue48.3
Superior colliculitissue45.4
Hypothalamustissue41.1
Hippocampal formationtissue31.8
Corpus callosumtissue29.4
Thymustissue28.7
Amygdalatissue28.2
Smooth muscletissue27.8medium
Endometrium 1tissue27.2not detected
Salivary glandtissue26.4not detected
Septumtissue26.2
Adipose tissuetissue25.6low
Lymph nodetissue25.5not detected
Ventral forebraintissue22.2
Cerebellumtissue21.4not detected
Basal gangliatissue21.1medium
Spleentissue20.4not detected
Seminal vesicletissue20.2not detected
Cerebral cortextissue20.1medium
Motor cortextissue20.1
Temporal cortextissue19.6
Insular cortextissue19.4
Putamentissue19.1
Entorhinal cortextissue18.7
Prefrontal cortextissue18.0
Tonsiltissue18.0not detected
Retrosplenial cortextissue18.0
Retrosplenial and cingulate cortextissue17.6
Bone marrowtissue17.1
Somatosensory cortextissue17.1
Occipital cortextissue16.2
Epididymistissue15.5not detected
Olfactory bulbtissue15.5
Fallopian tubetissue14.5not detected
Placentatissue13.9not detected
Appendixtissue13.7not detected
Vaginatissue13.5not detected
Lungtissue13.5medium
Cervixtissue13.4not detected
Prostatetissue12.6not detected
Esophagustissue12.5not detected
Urinary bladdertissue12.0not detected
Skin 1tissue10.9not detected
Skeletal muscletissue10.7not detected
Tonguetissue10.7
Gallbladdertissue9.0
Kidneytissue8.9not detected
Caudate putamentissue8.8
Frontal cortextissue8.7

Brain sub-regions (HPA Brain Atlas): detected in 190; highest nTPM — Area postrema (378.8), Posterior thalamic nucleus (372.9), Globus pallidus, externus (356.0), Inferior olive (330.4), Nucleus rhomboideus (324.8).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting ITPKB by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 138 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-548AN99.9770.912817
HSA-MIR-426799.9666.532368
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-652-5P99.9167.49505
HSA-MIR-454-3P99.9174.011925
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-17-5P99.8973.832665
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.34, missense Z -0.124 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000429204 splits into 2 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
1:226,634,674–226,735,528248 / 396.70.63no
1:226,735,529–226,737,458992 / 853.81.16no

Literature-anchored findings (GeneRIF, showing 15)

  • results highlight the potential role of the three isoforms of InsP3 3-kinase as direct InsP3 metabolizing enzymes and direct regulators of Ca2+ responses to extracellular signals (PMID:12747803)
  • We aim to summarize the existing information about functionally uncoupled IP(3)R and RyR channels, and to discuss the concept that those channels can participate in Ca(2+)-leak pathways. (PMID:16354157)
  • In each of the three isoforms a nuclear export signal has evolved in the catalytic domain either de novo (IP3K-A) or as a substitute for an earlier evolved corresponding N-terminal signal (IP3K-B and IP3K-C). (PMID:16740130)
  • IP3KB not only regulates cytoplasmic Ca(2+) signals by phosphorylation of subplasmalemmal and cytoplasmic Ins(1,4,5)P(3) but may also be involved in modulating nuclear Ca(2+) signals generated from these nuclear envelope invaginations. (PMID:21148483)
  • a specific increase in inositol 1,4,5-trisphosphate 3-kinase A and B (ITPKA and ITPKB) was observed upon hESCs spontaneous differentiation. (PMID:22446005)
  • ITPKB is increased in Alzheimer’s brain three-fold in the cerebral cortex of most patients with Alzheimer’s disease compared with control subjects and accumulates in dystrophic neurites associated with amyloid plaques. (PMID:24401760)
  • The authors confirm downregulation of miR-132 and upregulation of ITPKB in three distinct human Alzheimer’s disease patient cohorts. (PMID:27485122)
  • miR-140-5p regulates this context-specific autophagy through its target, inositol 1,4,5-trisphosphate kinase 2 (IP3k2). Therefore, the results of the present study demonstrated that miR-140-5p mediated drug-resistance in osteosarcoma cells by inducing autophagy. (PMID:27582507)
  • ITPKB does not affect the cellular actin structure and does not suppress dissemination of human lung cancer cells in mice. (PMID:29871874)
  • study also suggests a distinctive signaling function of IP4 that regulates NOX4. Furthermore, pharmaceutical inhibition of ITPKB displayed synergistic attenuation of tumor growth with cisplatin, suggesting ITPKB as a promising synthetic lethal target for cancer therapeutic intervention to overcome cisplatin resistance. (PMID:31081803)
  • Severe combined immunodeficiency caused by inositol-trisphosphate 3-kinase B (ITPKB) deficiency. (PMID:31987846)
  • Association of ITPKB, IL1R2 and COQ7 with Parkinson’s disease in Taiwan. (PMID:34244037)
  • Increased Levels of the Parkinson’s Disease-Associated Gene ITPKB Correlate with Higher Expression Levels of alpha-Synuclein, Independent of Mutation Status. (PMID:36768321)
  • Genome-Wide Meta-Analysis Identifies Multiple Novel Rare Variants to Predict Common Human Infectious Diseases Risk. (PMID:37108169)
  • Suppression of ITPKB degradation by Trim25 confers TMZ resistance in glioblastoma through ROS homeostasis. (PMID:38438346)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_rerioitpkbENSDARG00000010059
mus_musculusItpkbENSMUSG00000038855
rattus_norvegicusItpkbENSRNOG00000002969
drosophila_melanogasterIP3K1FBGN0032147
drosophila_melanogasterIp6kFBGN0034644
caenorhabditis_eleganslfe-2WBGENE00002979
caenorhabditis_elegansF30A10.3WBGENE00009262

Paralogs (6): IP6K2 (ENSG00000068745), ITPKC (ENSG00000086544), ITPKA (ENSG00000137825), IPMK (ENSG00000151151), IP6K3 (ENSG00000161896), IP6K1 (ENSG00000176095)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:109235) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 21 distinct phenotype terms.

Mouse phenotype (MP)Records
arrested T cell differentiation2
sparse hair1
absent CD8-positive, alpha-beta T cells1
distended abdomen1
decreased locomotor activity1
postnatal growth retardation1
decreased IgG level1
abnormal thymus involution1
premature death1
abnormal T cell physiology1
absent CD4-positive, alpha-beta T cells1
abnormal thymocyte activation1
increased susceptibility to parasitic infection1
diarrhea1
increased double-positive T cell number1
absent T cells1
decreased IgG1 level1
decreased IgG2a level1
decreased IgG2b level1
distended stomach1
absent thymus medulla1

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
ITPKB-IT1ncRNA100506443
STUMprotein-coding375057
PSEN2protein-coding5664

Protein

Protein identifiers

Inositol-trisphosphate 3-kinase B — P27987 (reviewed: P27987)

Alternative names: Inositol 1,4,5-trisphosphate 3-kinase B

All UniProt accessions (1): P27987

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the phosphorylation of 1D-myo-inositol 1,4,5-trisphosphate (InsP3) into 1D-myo-inositol 1,3,4,5-tetrakisphosphate and participates to the regulation of calcium homeostasis.

Subunit / interactions. Interacts with DMTN.

Subcellular location. Cytoplasm. Cytoskeleton. Endoplasmic reticulum.

Activity regulation. IP3K is activated by calcium and calmodulin. Form B is much more sensitive to calcium/calmodulin than form A.

Similarity. Belongs to the inositol phosphokinase (IPK) family.

Isoforms (2)

UniProt IDNamesCanonical?
P27987-11yes
P27987-22

RefSeq proteins (2): NP_001375333, NP_002212* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR005522IPKFamily
IPR038286IPK_sfHomologous_superfamily

Pfam: PF03770

Enzyme classification (BRENDA)

  • EC 2.7.1.127 — inositol-trisphosphate 3-kinase (BRENDA: 14 organisms, 87 substrates, 104 inhibitors, 42 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
1D-MYO-INOSITOL 1,4,5-TRISPHOSPHATE0.0002–0.01121
ATP0.033–2.513
1D-MYO-INOSITOL 2,4,5-TRISPHOSPHATE0.0015–0.0052
INSP30.0002–0.00172

Catalyzed reactions (Rhea)

  • 1D-myo-inositol 1,4,5-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + H(+) (RHEA:11020)

UniProt features (36 total): binding site 10, region of interest 6, compositionally biased region 5, modified residue 5, sequence conflict 4, sequence variant 3, chain 1, splice variant 1, mutagenesis site 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P27987-F156.580.25

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Transferases, Metabolic proteins, Predicted intracellular proteins, Cancer-related genes, Mutated cancer genes

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH enhanced · IF approved

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (10)

PositionRole
679ATP
690ATP
730–732ATP
743ATP
745substrate
766substrate
793–800substrate
817ATP
897ATP
900substrate

Post-translational modifications (5)

TypePositions
Phosphoserine43, 49, 71, 204, 269

Mutagenesis-validated functional residues (1)

PositionPhenotype
897loss of kinase activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 3; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

3 pathways:

IDPathwayEvidence
R-HSA-1855204Synthesis of IP3 and IP4 in the cytosolcurated
R-HSA-1483249Inositol phosphate metabolism—
R-HSA-1430728Metabolism—

MSigDB gene sets: 359 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_CELL_ACTIVATION, RNGTGGGC_UNKNOWN, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLINOSITOL_METABOLIC_PROCESS, HNF3ALPHA_Q6, GOBP_REGULATION_OF_ALPHA_BETA_T_CELL_ACTIVATION, GOBP_POSITIVE_REGULATION_OF_HEMOPOIESIS, GOBP_MYELOID_CELL_HOMEOSTASIS, GOBP_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS, GOBP_THYMIC_T_CELL_SELECTION, CMYB_01, GOBP_INOSITOL_PHOSPHATE_METABOLIC_PROCESS, GOBP_ALPHA_BETA_T_CELL_DIFFERENTIATION, GOBP_POLYOL_METABOLIC_PROCESS

GO Biological Process (5): signal transduction (GO:0007165), inositol trisphosphate metabolic process (GO:0032957), inositol phosphate biosynthetic process (GO:0032958), phosphatidylinositol phosphate biosynthetic process (GO:0046854), cellular response to calcium ion (GO:0071277)

GO Molecular Function (8): inositol hexakisphosphate kinase activity (GO:0000828), calmodulin binding (GO:0005516), ATP binding (GO:0005524), inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440), nucleotide binding (GO:0000166), protein binding (GO:0005515), kinase activity (GO:0016301), transferase activity (GO:0016740)

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), cytoskeleton (GO:0005856), membrane (GO:0016020)

Reactome top-level categories

2 top-level categories:

CategoryPathways
Inositol phosphate metabolism1
Metabolism1

GO top-level categories

29 GO namespaces:

CategoryTerms
cellular anatomical structure3
inositol phosphate metabolic process2
intracellular membrane-bounded organelle2
cytoplasm2
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
polyol biosynthetic process1
organophosphate biosynthetic process1
glycerophospholipid biosynthetic process1
response to calcium ion1
cellular response to metal ion1
phosphotransferase activity, phosphate group as acceptor1
inositol phosphate kinase activity1
protein binding1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
anion binding1
inositol trisphosphate kinase activity1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
transferase activity, transferring phosphorus-containing groups1
catalytic activity1
intracellular anatomical structure1
endomembrane system1
intracellular membraneless organelle1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 7 of 19 annotations. The rest are phylogenetic / computational / electronic (IEA).

7 experimentally-supported GO terms:

GO termNSEvidence
cellular response to calcium ionBPdirect assay
inositol trisphosphate metabolic processBPdirect assay
phosphatidylinositol phosphate biosynthetic processBPdirect assay
cytoplasmCCdirect assay
cytoskeletonCCdirect assay
endoplasmic reticulumCCdirect assay
inositol-1,4,5-trisphosphate 3-kinase activityMFdirect assay

Protein interactions and networks

STRING

showing 16 of 710 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
ITPKBIP6K1Q92551771
ITPKBIP6K3Q96PC2743
ITPKBIP6K2Q9UHH9663
ITPKBAKT1P31749536
ITPKBPLCG1P19174513
ITPKBGNA13Q14344493
ITPKBIPMKQ8NFU5490
ITPKBINPP5AQ14642487
ITPKBLCP2Q13094477
ITPKBZAP70P43403456
ITPKBMFHAS1Q9Y4C4442
ITPKBCALM1P02593429
ITPKBPIK3C3Q8NEB9428
ITPKBCALML6Q8TD86416
ITPKBCALML5Q9NZT1416
ITPKBCALML4Q96GE6416

IntAct

Human interaction partners of ITPKB in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

18 partners by confidence:

PartnerInteraction typeMIscoreRecords
GOLGA2physical association0.6704
BRAFphysical association0.6003
CTDSP1physical association0.5605
UBQLN2physical association0.5605
CEP70physical association0.5603
IFT88physical association0.5603
KRT34physical association0.5603
PPP3CAphysical association0.5603
SCAIphysical association0.5603
TRIM54physical association0.5603
PSME3physical association0.3701
SMAD4proximity0.2704
SPOPproximity0.2704
AKT1proximity0.2701
EGFRproximity0.2701
PTENproximity0.2701
PTPN11proximity0.2701
TP53proximity0.2701

BioGRID (29 interactions; top human partners by supporting records): GOLGA2 (Two-hybrid; 2 records), ADNP2 (Affinity Capture-MS), AKT1 (Biochemical Activity), CEP70 (Two-hybrid), CTDSP1 (Two-hybrid), DDX39A (Affinity Capture-RNA), ELAVL1 (Affinity Capture-RNA), ESF1 (Affinity Capture-MS), ESR2 (Affinity Capture-MS), HNRNPL (Affinity Capture-RNA), IFT88 (Two-hybrid), KIAA1429 (Affinity Capture-RNA), KRT34 (Two-hybrid), NR3C1 (Proximity Label-MS), NUDT21 (Affinity Capture-RNA)

SIGNOR signaling

2 signaling interactions:

AEffectBMechanism
PRKCA“down-regulates activity”ITPKB
PRKACA“down-regulates activity”ITPKBphosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 18 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.

GO biological processes:

GO termPartnersFoldFDR
positive regulation of gene expression510.8×5e-03

Disease & clinical

Genetic variants

Variant evidence for ITPKB: 159 ClinVar records (0 pathogenic / likely pathogenic); 13 GWAS associations.

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance116
Likely benign15
Benign8

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 45 predictions of 1,200):

Position(s)EffectΔscoreSites
1:226634887–226634888acceptor_loss1.00005
1:226637677–226637678donor_loss1.00005
1:226637751–226637752acceptor_loss1.00005
1:226639555–226639556donor_loss1.00005
1:226639659–226639660acceptor_loss1.00004
1:226641919–226641920donor_loss1.00005
1:226647165–226647166donor_loss1.00005
1:226647381–226647382acceptor_loss1.00004
1:226648772–226648773acceptor_loss1.00006
1:226634887acceptor_loss0.9900

AlphaMissense

1,823 missense substitutions predicted likely pathogenic (of 6,164 scored), across 377 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M77390.9540.998
M79790.9530.998
M72990.9200.997
M76990.9170.993
M89590.9170.998
M74290.8790.996
M65490.8590.978
M70490.8550.969
M74690.8360.991
D74380.9991.000
D89780.9991.000
H67680.9930.999
F68080.9931.000
F89880.9930.999
F88380.9881.000
H87480.9810.998
F81180.9800.999
F87180.9800.998
D76880.9790.995
D92380.9790.997

HPA cancer prognostics

RNA cancer specificity: Cancer enhanced (Skin Cutaneous Melanoma)

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

CancerPrognosticp-value
Kidney Renal Clear Cell Carcinoma (TCGA)favorable7.25e-06
Kidney Renal Clear Cell Carcinoma (validation)favorable0.000237

Disease associations

OMIM: gene MIM:147522 | disease phenotypes:

GenCC curated gene-disease

2 curated gene-disease records:

DiseaseClassificationInheritanceRecords
severe combined immunodeficiencyLimitedAutosomal recessive
Tourette syndromeNo Known Disease RelationshipUnknown

ClinGen Gene-Disease Validity

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

1 validity classifications:

DiseaseClassificationInheritance
ITPKB deficiencyLimitedAR

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (2 panels, 0 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

2 panels:

PanelRating
COVID-19 researchamber
Primary immunodeficiency or monogenic inflammatory bowel diseaseamber

Mondo (1): severe combined immunodeficiency (MONDO:0015974)

GWAS associations

13 associations:

StudyTraitp-value
GCST009325_8Parkinson’s disease or first degree relation to individual with Parkinson’s disease1e-15
GCST90002382_77Eosinophil percentage of white cells4e-13
GCST010002_7Refractive error1e-12
GCST004902_14Parkinson’s disease2e-11
GCST012490_422Femur bone mineral density x serum urate levels interaction4e-11
GCST010043_118Asthma2e-10
GCST010049_4Parkinson’s disease8e-10
GCST005038_75Allergic disease (asthma, hay fever or eczema)2e-9
GCST010042_29Asthma2e-9
GCST008306_4Dentures1e-8
GCST008295_13Number of decayed, missing and filled tooth surfaces or use of dentures3e-8
GCST010991_15Parkinson’s disease6e-8
GCST001521_6Subcutaneous adipose tissue6e-6

EFO canonical traits (from GWAS)

3 canonical traits:

EFO IDTrait name
EFO:0010078dentures
EFO:0004531urate measurement
EFO:0007991eosinophil percentage of leukocytes

MeSH disease descriptors

2 disease descriptors:

DescriptorNameTree numbers
D016511Severe Combined ImmunodeficiencyC16.320.798.750; C16.614.815; C18.452.284.800; C20.673.795.750
D005879Tourette SyndromeC10.228.140.079.898; C10.228.662.825.800; C10.574.500.850; C16.320.400.820; F03.625.992.850

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5165 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

GtoPdb / IUPHAR curated pharmacology

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

Target class: enzyme — Inositol 1,4,5-trisphosphate 3-kinases

Most potent curated ligand interactions (1 total), top 1:

LigandActionAffinityParameter
GNF362Inhibition8.05pIC50

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases expression3
Valproic Acidaffects expression, decreases expression3
bisphenol Adecreases methylation, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tobacco Smoke Pollutiondecreases expression, decreases methylation2
GSK-J4increases expression1
FR900359decreases phosphorylation1
methylmercuric chlorideincreases expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
trichostatin Aaffects cotreatment, increases expression1
ochratoxin Aincreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment, decreases expression1
avobenzoneincreases expression1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression1
dorsomorphinincreases expression, affects cotreatment1
Sunitinibdecreases expression1
Acetaminophenincreases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Air Pollutantsaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation, increases methylation1
Doxorubicindecreases expression1
Leadaffects expression1
Lipopolysaccharidesdecreases expression, affects response to substance, increases expression, affects cotreatment1
Methapyrileneincreases methylation1
Ozoneaffects cotreatment, decreases expression, increases abundance1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3721023BindingInhibition of ITPKb in human Jurkat cells assessed as reduction in conversion of IP3 to IP4 using [3H]-myo-inositol incubated for 5 mins by beta-RAM radio-HPLC methodCompounds and compositions as ITPKB inhibitors

Cellosaurus cell lines

4 cell lines: 3 cancer cell line, 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_D7STUbigene A-549 ITPKB KOCancer cell lineMale
CVCL_D8NKUbigene HCT 116 ITPKB KOCancer cell lineMale
CVCL_D9HKUbigene HEK293 ITPKB KOTransformed cell lineFemale
CVCL_E0FPUbigene HeLa ITPKB KOCancer cell lineFemale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 278 trials:

NCTPhaseStatusTitle
NCT00152750Phase 4UNKNOWNStudy of Clonidine on Sleep Architecture in Children With Tourette’s Syndrome (TS) and Comorbid ADHD
NCT00226824Phase 4TERMINATEDSafety Study of Galantamine in Tic Disorders
NCT00241176Phase 4COMPLETEDOpen Label Trial of Aripiprazole in Children and Adolescents With Tourette’s Disorder
NCT00370838Phase 4COMPLETEDComparison of Keppra and Clonidine in the Treatment of Tics
NCT01018056Phase 4COMPLETEDDeveloping New Treatments for Tourette Syndrome: Therapeutic Trials With Modulators of Glutamatergic Neurotransmission
NCT01547000Phase 4COMPLETEDGuanfacine in Children With Tic Disorders
NCT03239210Phase 4COMPLETEDEffects of Ondansetron in Obsessive-compulsive and Tic Disorders
NCT00004376Phase 3COMPLETEDPhase III Randomized, Double-Blind, Placebo-Controlled Study of Guanfacine for Tourette Syndrome and Attention Deficit Hyperactivity Disorder
NCT00206323Phase 3COMPLETEDA Randomized, Placebo-controlled, Tourette Syndrome Study.
NCT00206336Phase 3COMPLETEDAn Open-label Study to Determine the Efficacy and Safety of Topiramate in the Treatment of Tourette Syndrome.
NCT00478842Phase 3COMPLETEDPallidal Stimulation and Gilles de la Tourette Syndrome
NCT00681863Phase 3TERMINATEDOpen-label Extension Study of Pramipexole in the Treatment of Children and Adolescents With Tourette Syndrome
NCT01501695Phase 3COMPLETEDPhase III Study of 5LGr to Treat Tic Disorder
NCT03087201Phase 3COMPLETEDCANNAbinoids in the Treatment of TICS (CANNA-TICS)
NCT03487783Phase 3COMPLETEDAripiprazole Oral Solution in the Treatment of Children and Adolescents With Tourette’s Syndrome
NCT03567291Phase 3TERMINATEDEvaluation of Safety and Tolerability of Long-term TEV-50717 (Deutetrabenazine) for Treatment of Tourette Syndrome in Children and Adolescents
NCT03571256Phase 3COMPLETEDA Study to Test if TEV-50717 is Effective in Relieving Tics Associated With Tourette Syndrome (TS)
NCT06021522Phase 3ACTIVE_NOT_RECRUITINGA Study to Evaluate Long-term Safety of Ecopipam Tablets in Children, Adolescents and Adults With Tourette’s Disorder
NCT00220766Phase 3COMPLETEDRapid Infusion of Immune Globulin Intravenous (Human) In Primary Immunodeficiency Patients
NCT01420627Phase 3COMPLETEDEZN-2279 in Patients With ADA-SCID
NCT06940570Phase 3SUSPENDEDMethadone as an Alternative Treatment for Children Underdoing HSCT
NCT00322101Phase 3COMPLETEDLow-Dose or High-Dose Conditioning Followed by Peripheral Blood Stem Cell Transplant in Treating Patients With Myelodysplastic Syndrome or Acute Myelogenous Leukemia
NCT00799461Phase 3COMPLETEDInternet-Based Program With or Without Telephone-Based Problem-Solving Training in Helping Long-Term Survivors of Hematopoietic Stem Cell Transplant Cope With Late Complications
NCT01305200Phase 3COMPLETEDSupersaturated Calcium Phosphate Rinse in Preventing Oral Mucositis in Young Patients Undergoing Autologous or Donor Stem Cell Transplant
NCT00004393Phase 2COMPLETEDPhase II Double Blind Placebo Controlled Trial of Risperidone in Tourette Syndrome
NCT00004652Phase 2COMPLETEDPhase II Pilot Controlled Study of Short Vs Longer Term Pimozide (Orap) Therapy in Tourette Syndrome
NCT00231985Phase 2COMPLETEDEffectiveness of Behavior Therapy and Psychosocial Therapy for the Treatment of Tourette Syndrome and Chronic Tic Disorder
NCT00311909Phase 2COMPLETEDThalamic Deep Brain Stimulation for Tourette Syndrome
NCT00529308Phase 2COMPLETEDTranscranial Magnetic Stimulation (TMS) for Individuals With Tourette’s Syndrome
NCT00558467Phase 2COMPLETEDPramipexole Pilot Phase II Study in Children and Adolescents With Tourette Disorder According to DSM-IV Criteria
NCT01043549Phase 2TERMINATEDRepetitive Transcranial Magnetic Stimulation of the Posterior Parietal Cortex in Patients Suffering From Gilles de la Tourette Syndrome
NCT01133353Phase 2WITHDRAWNA Study of the Effectiveness and Safety of Tetrabenazine MR in Pediatric Subjects With Tourette’s Syndrome
NCT01475383Phase 2WITHDRAWNStudy Evaluating The Safety And Efficacy Of PF-03654746 In Adult Subjects With Tourette’s Syndrome
NCT01647269Phase 2COMPLETEDA Trial of Bilateral Deep Brain Stimulation to the Globus Pallidus Internum in Tourette Syndrome
NCT01904773Phase 2COMPLETEDSafety, Tolerability, Pharmacokinetic, and Efficacy Study of AZD5213 in Adolescents With Tourette’s Disorder
NCT02102698Phase 2COMPLETEDEcopipam Treatment of Tourette’s Syndrome in Subjects 7-17 Years
NCT02217007Phase 2WITHDRAWNA Trial Evaluating the Efficacy, Safety, and Pharmacokinetics of SNC-102 in Subjects With Tourette Syndrome
NCT02247206Phase 2COMPLETEDVoIP Delivered Behavior Therapy for Tourette Syndrome
NCT02581865Phase 2COMPLETEDSafety and Efficacy Study of NBI-98854 in Adults With Tourette Syndrome
NCT02619084Phase 2COMPLETEDSubthalamic Stimulation in Tourette’s Syndrome
NCT02679079Phase 2COMPLETEDSafety and Efficacy Study of NBI-98854 in Children and Adolescents With Tourette Syndrome
NCT02879578Phase 2COMPLETEDSafety and Tolerability Study of NBI-98854 for the Treatment of Subjects With Tourette Syndrome
NCT03066193Phase 2COMPLETEDEfficacy of a Therapeutic Combination of Dronabinol and PEA for Tourette Syndrome
NCT03247244Phase 2TERMINATEDSafety and Efficacy of Cannabis in Tourette Syndrome
NCT03325010Phase 2COMPLETEDSafety, Tolerability, and Efficacy of NBI-98854 for the Treatment of Pediatric Subjects With Tourette Syndrome
NCT03444038Phase 2COMPLETEDOpen-Label Safety and Tolerability Study of NBI-98854 for the Treatment of Pediatric Subjects With Tourette Syndrome
NCT03530293Phase 2TERMINATEDSafety and Efficacy of NBI-98854 in Pediatric Subjects With Tourette Syndrome
NCT03625453Phase 2COMPLETEDStudy of ABX-1431 in Adult Patients With Tourette Syndrome or Chronic Motor Tic Disorder
NCT03651726Phase 2UNKNOWNA Study to Examine the Efficacy of a Therapeutic THX-110 for Tourette Syndrome
NCT03732534Phase 2TERMINATEDRollover Study for Continuing NBI-98854 Administration in Pediatric Subjects With Tourette Syndrome
NCT03944447Phase 2UNKNOWNOutcomes Mandate National Integration With Cannabis as Medicine
NCT04007991Phase 2COMPLETEDEcopipam Tablets to Study Tourette’s Syndrome in Children and Adolescents
NCT04354103Phase 2TERMINATEDAtomoxetine in Patients With Tourette’s Syndrome
NCT04978428Phase 2COMPLETEDEpidiolex in Obsessive Compulsive Disorder and Related Disorders
NCT05126888Phase 2NOT_YET_RECRUITINGSCI-110 in the Treatment of Tourette Syndrome
NCT05434546Phase 2COMPLETEDA Study to Explore the Effect of Sepranolone in Tourette Syndrome
NCT06081348Phase 2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06194305Phase 2RECRUITINGMultimodal Profiling of Response to Pediatric Comprehensive Behavioral Intervention for Tics
NCT06315751Phase 2ACTIVE_NOT_RECRUITINGEfficacy and Safety of Gemlapodect (NOE-105) in Adults and Adolescents With Tourette Syndrome
NCT06678737Phase 2RECRUITINGCBIT+TMS R33 Phase