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ITPK1 inositol-tetrakisphosphate 1-kinase [ Homo sapiens (human) ]

Gene ID: 3705, updated on 14-Nov-2024

Summary

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Official Symbol
ITPK1provided by HGNC
Official Full Name
inositol-tetrakisphosphate 1-kinaseprovided by HGNC
Primary source
HGNC:HGNC:6177
See related
Ensembl:ENSG00000100605 MIM:601838; AllianceGenome:HGNC:6177
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
ITRPK1
Summary
This gene encodes an enzyme that belongs to the inositol 1,3,4-trisphosphate 5/6-kinase family. This enzyme regulates the synthesis of inositol tetraphosphate, and downstream products, inositol pentakisphosphate and inositol hexakisphosphate. Inositol metabolism plays a role in the development of the neural tube. Disruptions in this gene are thought to be associated with neural tube defects. A pseudogene of this gene has been identified on chromosome X. [provided by RefSeq, Jul 2016]
Expression
Ubiquitous expression in brain (RPKM 29.9), fat (RPKM 26.2) and 25 other tissues See more
Orthologs
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Genomic context

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See ITPK1 in Genome Data Viewer
Location:
14q32.12
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (92936914..93115925, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (87168906..87347917, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (93403259..93582270, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:93377003-93377546 Neighboring gene long intergenic non-protein coding RNA 2287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93403665-93404166 Neighboring gene uncharacterized LOC124903366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93418215-93418715 Neighboring gene chromogranin A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93428049-93428613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93439689-93440278 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93440279-93440866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93440867-93441454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93459858-93460540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93465116-93465630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93472927-93473838 Neighboring gene Sharpr-MPRA regulatory region 15213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93475437-93475938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93477163-93477664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93477665-93478164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93480925-93481426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93481427-93481926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93482386-93482886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93484819-93485602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93485603-93486386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93500760-93501455 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93506655-93507584 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93511809-93512368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93515290-93515917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93516545-93517172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93522559-93523246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93543288-93543801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93544610-93545178 Neighboring gene ITPK1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93550988-93551611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93554107-93554728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93558517-93559024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93564664-93565656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93604409-93604908 Neighboring gene cytochrome b5 type A pseudogene 3 Neighboring gene modulator of apoptosis 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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?
  1. Genetic Effects of ITPK1 Polymorphisms on the Risk of Neural Tube Defects: a Population-Based Study.
    Title: Genetic Effects of ITPK1 Polymorphisms on the Risk of Neural Tube Defects: a Population-Based Study.
  2. ITPK1 role in the lipid-independent synthesis of inositol phosphates.
    Title: ITPK1 mediates the lipid-independent synthesis of inositol phosphates controlled by metabolism.
  3. The results suggested that the maternal rs3783903 of ITPK1 might be associated with spina bifida, and the allele G of rs3783903 might affect the binding of AP-1 and the decrease of maternal plasma inositol hexakisphosphate concentration.
    Title: The maternal ITPK1 gene polymorphism is associated with neural tube defects in a high-risk Chinese population.
  4. Activation of PLC by an endogenous cytokine (GBP) in Drosophila S3 cells and its application as a model for studying inositol phosphate signalling through ITPK1.
    Title: Activation of PLC by an endogenous cytokine (GBP) in Drosophila S3 cells and its application as a model for studying inositol phosphate signalling through ITPK1.
  5. HEK293 cells stably expressing acetylated ITPK1 had reduced levels of the higher phosphorylated forms of inositol, compared with the levels seen in cells expressing unacetylated ITPK1
    Title: Regulation of inositol 1,3,4-trisphosphate 5/6-kinase (ITPK1) by reversible lysine acetylation.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
  8. analysis of inositol phosphate signaling pathway integration via human ITPK1
    Title: Integration of inositol phosphate signaling pathways via human ITPK1.
  9. 5/6-kinase modifies TNFalpha-induced apoptosis by interfering with the activation of TNF-R1-associated death domain
    Title: Inositol 1,3,4-trisphosphate 5/6-kinase inhibits tumor necrosis factor-induced apoptosis.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
EBI GWAS Catalog
Genome-wide association study link novel loci to endometriosis.
EBI GWAS Catalog
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables catalytic activity TAS
Traceable Author Statement
more info
 PubMed 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables inositol-1,3,4,5-tetrakisphosphate 6-kinase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables inositol-1,3,4-trisphosphate 5-kinase activity EXP
Inferred from Experiment
more info
 PubMed 
enables inositol-1,3,4-trisphosphate 5-kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables inositol-1,3,4-trisphosphate 6-kinase activity EXP
Inferred from Experiment
more info
 PubMed 
enables inositol-1,3,4-trisphosphate 6-kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables inositol-3,4,5,6-tetrakisphosphate 1-kinase activity EXP
Inferred from Experiment
more info
 PubMed 
enables inositol-3,4,5,6-tetrakisphosphate 1-kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables inositol-3,4,6-trisphosphate 1-kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables isomerase activity IEA
Inferred from Electronic Annotation
more info
  
enables magnesium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in blood coagulation TAS
Traceable Author Statement
more info
  
involved_in inositol trisphosphate metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in necroptotic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neural tube development IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in apical plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
inositol-tetrakisphosphate 1-kinase
Names
inositol 1,3,4-trisphosphate 5/6-kinase
ins(1,3,4)P(3) 5/6-kinase
NP_001136065.1
NP_001136066.1
NP_001350636.1
NP_055031.2
XP_016876751.2
XP_047287307.1
XP_054184951.1
XP_054184952.1
XP_054231975.1
XP_054231976.1

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

  1. NG_051071.1 RefSeqGene

    Range
    4995..184006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142593.3 → NP_001136065.1  inositol-tetrakisphosphate 1-kinase isoform a

    See identical proteins and their annotated locations for NP_001136065.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice pattern in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AA770154, AF279372, AL110118, AL117192, BC018192, BX407816, BX420122, U51336
    Consensus CDS
    CCDS9907.1
    UniProtKB/Swiss-Prot
    Q13572, Q9BTL6, Q9H2E7
    UniProtKB/TrEMBL
    Q8N3Y0
    Related
    ENSP00000451091.1, ENST00000556603.6
    Conserved Domains (1) summary
    pfam05770
    Location:1 → 318
    Ins134_P3_kin; Inositol 1, 3, 4-trisphosphate 5/6-kinase

  2. NM_001142594.3 → NP_001136066.1  inositol-tetrakisphosphate 1-kinase isoform b

    See identical proteins and their annotated locations for NP_001136066.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice pattern in the 3' coding region, compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AL110118, AL117192, BC003622, BX407816, BX420122
    Consensus CDS
    CCDS45157.1
    UniProtKB/TrEMBL
    B4DE87
    Related
    ENSP00000346272.3, ENST00000354313.7
    Conserved Domains (1) summary
    cl17255
    Location:1 → 301
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  3. NM_001363707.2 → NP_001350636.1  inositol-tetrakisphosphate 1-kinase isoform c

    Status: REVIEWED

    Source sequence(s)
    AL117192
    Consensus CDS
    CCDS86425.1
    UniProtKB/TrEMBL
    G3V4M9
    Conserved Domains (1) summary
    cl17255
    Location:1 → 199
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  4. NM_014216.6 → NP_055031.2  inositol-tetrakisphosphate 1-kinase isoform a

    See identical proteins and their annotated locations for NP_055031.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Both variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AA770154, AF279372, AL110118, AL117192, BC018192, BX407816, BX420122
    Consensus CDS
    CCDS9907.1
    UniProtKB/Swiss-Prot
    Q13572, Q9BTL6, Q9H2E7
    UniProtKB/TrEMBL
    Q8N3Y0
    Related
    ENSP00000267615.5, ENST00000267615.11
    Conserved Domains (1) summary
    pfam05770
    Location:1 → 318
    Ins134_P3_kin; Inositol 1, 3, 4-trisphosphate 5/6-kinase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    92936914..93115925 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431351.1 → XP_047287307.1  inositol-tetrakisphosphate 1-kinase isoform X1

    UniProtKB/TrEMBL
    G3V4M9
    Related
    ENSP00000451893.1, ENST00000555495.5

  2. XM_017021262.2 → XP_016876751.2  inositol-tetrakisphosphate 1-kinase isoform X1

    UniProtKB/TrEMBL
    G3V4M9

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187601.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    51476..230487 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328977.1 → XP_054184952.1  inositol-tetrakisphosphate 1-kinase isoform X1

    UniProtKB/TrEMBL
    G3V4M9

  2. XM_054328976.1 → XP_054184951.1  inositol-tetrakisphosphate 1-kinase isoform X1

    UniProtKB/TrEMBL
    G3V4M9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    87168906..87347917 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376001.1 → XP_054231976.1  inositol-tetrakisphosphate 1-kinase isoform X1

    UniProtKB/TrEMBL
    G3V4M9

  2. XM_054376000.1 → XP_054231975.1  inositol-tetrakisphosphate 1-kinase isoform X1

    UniProtKB/TrEMBL
    G3V4M9
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13572.2 GenPept UniProtKB/Swiss-Prot:Q13572

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