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    TPCN2 two pore segment channel 2 [ Homo sapiens (human) ]

    Gene ID: 219931, updated on 11-Apr-2024

    Summary

    Official Symbol
    TPCN2provided by HGNC
    Official Full Name
    two pore segment channel 2provided by HGNC
    Primary source
    HGNC:HGNC:20820
    See related
    Ensembl:ENSG00000162341 MIM:612163; AllianceGenome:HGNC:20820
    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
    TPC2; SHEP10
    Summary
    This gene encodes a putative cation-selective ion channel with two repeats of a six-transmembrane-domain. The protein localizes to lysosomal membranes and enables nicotinic acid adenine dinucleotide phosphate (NAADP) -induced calcium ion release from lysosome-related stores. This ubiquitously expressed gene has elevated expression in liver and kidney. Two common nonsynonymous SNPs in this gene strongly associate with blond versus brown hair pigmentation.[provided by RefSeq, Dec 2009]
    Expression
    Ubiquitous expression in skin (RPKM 3.4), endometrium (RPKM 3.2) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TPCN2 in Genome Data Viewer
    Location:
    11q13.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (69048932..69090597)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (69059173..69101661)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (68816400..68858065)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MRGPRF antisense RNA 1 Neighboring gene MAS related GPR family member F Neighboring gene uncharacterized LOC124902701 Neighboring gene uncharacterized LOC124902702 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68807523-68808024 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68808025-68808524 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68811813-68812480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3689 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68818804-68819378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68820529-68821102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68833413-68834165 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:68847233-68848432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68853053-68853554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68853555-68854054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3690 Neighboring gene microRNA 3164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68869613-68870113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68887863-68888491 Neighboring gene Sharpr-MPRA regulatory region 9006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68916179-68916678 Neighboring gene Sharpr-MPRA regulatory region 4947 Neighboring gene uncharacterized LOC338694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68922957-68923884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3692 Neighboring gene Sharpr-MPRA regulatory region 1080 Neighboring gene uncharacterized LOC105369366 Neighboring gene small integral membrane protein 38

    Genomic regions, transcripts, and products

    Expression

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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Skin/hair/eye pigmentation, variation in, 10
    MedGen: C2677088 OMIM: 612267 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Two newly identified genetic determinants of pigmentation in Europeans.
    EBI GWAS Catalog
    Web-based, participant-driven studies yield novel genetic associations for common traits.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: SMIM38

    Clone Names

    • FLJ41094

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables NAADP-sensitive calcium-release channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables NAADP-sensitive calcium-release channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables NAADP-sensitive calcium-release channel activity TAS
    Traceable Author Statement
    more info
     
    enables calcium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ligand-gated sodium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ligand-gated sodium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylinositol-3,5-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    NOT enables voltage-gated calcium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables voltage-gated calcium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT enables voltage-gated sodium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in calcium-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in calcium-mediated signaling IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in endocytosis involved in viral entry into host cell IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endocytosis involved in viral entry into host cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endosome to lysosome transport of low-density lipoprotein particle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in intracellular calcium ion homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular pH reduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lysosome organization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in monoatomic ion transmembrane transport TAS
    Traceable Author Statement
    more info
     
    involved_in negative regulation of developmental pigmentation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in receptor-mediated endocytosis of virus by host cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of autophagy IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in regulation of exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in release of sequestered calcium ion into cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to vitamin D IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smooth muscle contraction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sodium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endolysosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in melanosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of monoatomic ion channel complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    two pore channel protein 2
    Names
    two pore calcium channel protein 2
    voltage-dependent calcium channel protein TPC2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_016153.2 RefSeqGene

      Range
      5002..46667
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_139075.4NP_620714.2  two pore channel protein 2

      See identical proteins and their annotated locations for NP_620714.2

      Status: REVIEWED

      Source sequence(s)
      AP003071
      Consensus CDS
      CCDS8189.1
      UniProtKB/Swiss-Prot
      Q8NHX9, Q9NT82
      UniProtKB/TrEMBL
      A0A1B0GUM5
      Related
      ENSP00000294309.3, ENST00000294309.8
      Conserved Domains (1) summary
      pfam00520
      Location:468697
      Ion_trans; Ion transport protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      69048932..69090597
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      69059173..69101661
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)