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    PLCH2 phospholipase C eta 2 [ Homo sapiens (human) ]

    Gene ID: 9651, updated on 14-Nov-2024

    Summary

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    Official Symbol
    PLCH2provided by HGNC
    Official Full Name
    phospholipase C eta 2provided by HGNC
    Primary source
    HGNC:HGNC:29037
    See related
    Ensembl:ENSG00000149527 MIM:612836; AllianceGenome:HGNC:29037
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PLCL4; PLC-L4; PLCeta2; PLC-eta2
    Summary
    PLCH2 is a member of the PLC-eta family of the phosphoinositide-specific phospholipase C (PLC) superfamily of enzymes that cleave PtdIns(4,5) P2 to generate second messengers inositol 1,4,5-trisphosphate and diacylglycerol (Zhou et al., 2005 [PubMed 16107206]).[supplied by OMIM, Jun 2009]
    Expression
    Biased expression in skin (RPKM 13.2), brain (RPKM 3.0) and 10 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PLCH2 in Genome Data Viewer
    Location:
    1p36.32
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (2415943..2505532)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (1855498..1946621)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2398890..2436971)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MORN repeat containing 1 Neighboring gene small nuclear ribonucleoprotein polypeptide N pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2306674-2306868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 55 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 56 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 113 Neighboring gene Sharpr-MPRA regulatory region 13804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2340121-2340621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2342650-2343230 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:2343231-2343811 to GRCh37_chr1:2344393-2344972 Neighboring gene retention in endoplasmic reticulum sorting receptor 1 Neighboring gene peroxisomal biogenesis factor 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2361610-2361787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2377030-2377864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2378700-2379534 Neighboring gene Sharpr-MPRA regulatory region 13638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2383066-2383714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2383715-2384362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2423421-2423982 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:2430511-2431710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2454755-2455542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2458062-2458782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2459504-2460224 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:2460225-2460944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2461459-2461962 Neighboring gene pantothenate kinase 4 (inactive) Neighboring gene hes family bHLH transcription factor 5

    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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    Related articles in PubMed

    1. Activation of human phospholipase C-eta2 by Gbetagamma. Zhou Y, et al. Biochemistry, 2008 Apr 15. PMID 18361507, Free PMC Article
    2. Role of phosphoinositide-specific phospholipase C η2 in isolated and syndromic mental retardation. Lo Vasco VR. Eur Neurol, 2011. PMID 21474938
    3. Investigating SNPs flanking the D1S80 locus in a Tamil population from India. Balamurugan K, et al. Hum Biol, 2010 Apr. PMID 20649401
    4. Molecular cloning and characterization of PLC-eta2. Zhou Y, et al. Biochem J, 2005 Nov 1. PMID 16107206, Free PMC Article
    5. Identification of a novel class of mammalian phosphoinositol-specific phospholipase C enzymes. Stewart AJ, et al. Int J Mol Med, 2005 Jan. PMID 15583837

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PLCH2 might be a putative candidate gene for the neurodevelopmental delay observed in patients bearing 1p36.3 deletions.
      Title: Role of phosphoinositide-specific phospholipase C η2 in isolated and syndromic mental retardation.
    2. The researchers investigated the D1S80 minisatellite and associated single nucelotide polymorphisms in a Tamil population in India.
      Title: Investigating SNPs flanking the D1S80 locus in a Tamil population from India.
    3. Purified Gbeta 1gamma 2 stimulated the activity of purified PLC-eta2 in a concentration-dependent manner similar to that observed with purified PLC-beta2.
      Title: Activation of human phospholipase C-eta2 by Gbetagamma.
    4. PLC(eta)2 is a neuron-specific isozyme that may be important for the formation and/or maintenance of the neuronal network in the postnatal brain
      Title: A novel phospholipase C, PLC(eta)2, is a neuron-specific isozyme.
    5. The molecular cloning and sequencing of phospholipase C eta2 are reported.
      Title: Molecular cloning and characterization of PLC-eta2.
    6. molecular cloning of PLC-eta1 and PLC-eta2
      Title: Identification of a novel class of mammalian phosphoinositol-specific phospholipase C enzymes.
    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 genome-wide association study in Chinese men identifies three risk loci for non-obstructive azoospermia.
    EBI GWAS Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 envelope glycoproteins gp120 and gp160 directly and specifically impair the CD3/TcR-mediated activation of phospholipase C (PLC) via the CD4 molecule in uninfected T cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Clone Names

    • RP3-395M20.1

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol phospholipase C activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol phospholipase C activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in lipid catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phosphatidylinositol-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phospholipase C-activating G protein-coupled receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in release of sequestered calcium ion into cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2
    Names
    phosphoinositide phospholipase C-eta-2
    phosphoinositide phospholipase C-like 4
    phospholipase C-eta2
    phospholipase C-like 4
    phospholipase C-like protein 4
    NP_001289941.1
    NP_001289942.1
    NP_055453.2
    XP_047290979.1
    XP_047290980.1
    XP_047290981.1
    XP_047290984.1
    XP_047290985.1
    XP_047290989.1
    XP_047290990.1
    XP_047290994.1
    XP_047290995.1
    XP_054184595.1
    XP_054195704.1
    XP_054195705.1
    XP_054195706.1
    XP_054195707.1
    XP_054195708.1
    XP_054195709.1
    XP_054195710.1
    XP_054195711.1
    XP_054195712.1

    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.

    mRNA and Protein(s)

    1. NM_001303012.2 → NP_001289941.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5'-terminal exon, uses an alternate start codon, and uses an alternate splice site in the 3' coding region, which results in a frameshift compared to variant 1. The encoded isoform (2) has shorter and distinct N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AB007919, AL139246, BM971622
      UniProtKB/TrEMBL
      Q86YU9
      Related
      ENSP00000397289.1, ENST00000449969.5
      Conserved Domains (7) summary
      cd00275
      Location:730 → 855
      C2_PLC_like; C2 domain present in Phosphoinositide-specific phospholipases C (PLC)
      cd08633
      Location:298 → 700
      PI-PLCc_eta2; Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta2
      PLN02952
      Location:215 → 840
      PLN02952; phosphoinositide phospholipase C
      cd00051
      Location:146 → 212
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      cd13364
      Location:22 → 128
      PH_PLC_eta; Phospholipase C-eta (PLC-eta) pleckstrin homology (PH) domain
      pfam09279
      Location:216 → 298
      EF-hand_like; Phosphoinositide-specific phospholipase C, efhand-like
      pfam13499
      Location:147 → 208
      EF-hand_7; EF-hand domain pair

    2. NM_001303013.1 → NP_001289942.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR, uses an alternate start codon, and uses an alternate splice site in the 3' coding region, which results in a frameshift compared to variant 1. The encoded isoform (3) has shorter and distinct N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AL139246, BC043358, BC144620, BM971622, DQ176850
      UniProtKB/Swiss-Prot
      O75038
      Conserved Domains (7) summary
      cd00275
      Location:777 → 902
      C2_PLC_like; C2 domain present in Phosphoinositide-specific phospholipases C (PLC)
      cd08633
      Location:345 → 747
      PI-PLCc_eta2; Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta2
      PLN02952
      Location:262 → 887
      PLN02952; phosphoinositide phospholipase C
      cd00051
      Location:193 → 259
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      cd13364
      Location:69 → 175
      PH_PLC_eta; Phospholipase C-eta (PLC-eta) pleckstrin homology (PH) domain
      pfam09279
      Location:263 → 345
      EF-hand_like; Phosphoinositide-specific phospholipase C, efhand-like
      pfam13499
      Location:194 → 255
      EF-hand_7; EF-hand domain pair

    3. NM_014638.4 → NP_055453.2  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform 1

      See identical proteins and their annotated locations for NP_055453.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL139246, BC043358, BX117873, DQ176850
      Consensus CDS
      CCDS59959.1
      UniProtKB/Swiss-Prot
      A2VCM3, B9DI80, O75038, Q3LUA8, Q86XJ2, Q86XU1, Q86YU7, Q8TEH5, Q8WUS6
      UniProtKB/TrEMBL
      B9DI82
      Related
      ENSP00000367747.3, ENST00000378486.8
      Conserved Domains (7) summary
      cd00275
      Location:757 → 882
      C2_PLC_like; C2 domain present in Phosphoinositide-specific phospholipases C (PLC)
      cd08633
      Location:325 → 727
      PI-PLCc_eta2; Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta2
      PLN02952
      Location:242 → 867
      PLN02952; phosphoinositide phospholipase C
      cd00051
      Location:173 → 239
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      cd13364
      Location:49 → 155
      PH_PLC_eta; Phospholipase C-eta (PLC-eta) pleckstrin homology (PH) domain
      pfam09279
      Location:243 → 325
      EF-hand_like; Phosphoinositide-specific phospholipase C, efhand-like
      pfam13499
      Location:174 → 235
      EF-hand_7; EF-hand domain pair

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      2415943..2505532
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435029.1 → XP_047290985.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X4

    2. XM_047435028.1 → XP_047290984.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X4

    3. XM_047435038.1 → XP_047290994.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X7

    4. XM_047435023.1 → XP_047290979.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X1

    5. XM_047435025.1 → XP_047290981.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X3

    6. XM_047435024.1 → XP_047290980.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X2

    7. XM_047435033.1 → XP_047290989.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X5

    8. XM_047435034.1 → XP_047290990.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X6

    9. XM_047435039.1 → XP_047290995.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X8

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187515.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      18641..56722
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328620.1 → XP_054184595.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      1855498..1946621
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339733.1 → XP_054195708.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X4

    2. XM_054339731.1 → XP_054195706.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X4

    3. XM_054339736.1 → XP_054195711.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X7

    4. XM_054339729.1 → XP_054195704.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X1

    5. XM_054339732.1 → XP_054195707.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X3

    6. XM_054339730.1 → XP_054195705.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X2

    7. XM_054339734.1 → XP_054195709.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X5

    8. XM_054339735.1 → XP_054195710.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X6

    9. XM_054339737.1 → XP_054195712.1  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75038.3 GenPept UniProtKB/Swiss-Prot:O75038

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