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

Gene ID: 219931, updated on 23-Nov-2023

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
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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 intracellular phosphatidylinositol-3,5-bisphosphate-sensitive monatomic cation channel activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables intracellular phosphatidylinositol-3,5-bisphosphate-sensitive 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)