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

Gene ID: 219931, updated on 17-Jun-2019

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
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

Genomic context

See TPCN2 in Genome Data Viewer
Location:
11q13.3
Exon count:
25
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (69048932..69090597)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (68816350..68858072)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MAS related GPR family member D Neighboring gene MRGPRF antisense RNA 1 Neighboring gene MAS related GPR family member F Neighboring gene uncharacterized LOC107984344 Neighboring gene microRNA 3164 Neighboring gene Sharpr-MPRA regulatory region 9006 Neighboring gene uncharacterized LOC338694 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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

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

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Ion channel transport, organism-specific biosystem (from REACTOME)
    Ion channel transport, organism-specific biosystemIon channels mediate the flow of ions across the plasma membrane of cells. They are integral membrane proteins, typically a multimer of proteins, which, when arranged in the membrane, create a pore f...
  • Pancreatic secretion, organism-specific biosystem (from KEGG)
    Pancreatic secretion, organism-specific biosystemThe pancreas performs both exocrine and endocrine functions. The exocrine pancreas consists of two parts, the acinar and duct cells. The primary functions of pancreatic acinar cells are to synthesiz...
  • Pancreatic secretion, conserved biosystem (from KEGG)
    Pancreatic secretion, conserved biosystemThe pancreas performs both exocrine and endocrine functions. The exocrine pancreas consists of two parts, the acinar and duct cells. The primary functions of pancreatic acinar cells are to synthesiz...
  • Stimuli-sensing channels, organism-specific biosystem (from REACTOME)
    Stimuli-sensing channels, organism-specific biosystemIon channels that mediate sensations such as pain, warmth, cold, taste pressure and vision. Channels that mediate these sensations include acid-sensing ion channels (ASICs) (Wang & Xu 2011, Qadri et ...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: SMIM38

Homology

Clone Names

  • FLJ41094

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NAADP-sensitive calcium-release channel activity IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
voltage-gated calcium channel activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
calcium-mediated signaling IGI
Inferred from Genetic Interaction
more info
PubMed 
cellular calcium ion homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
lysosome organization IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of autophagy IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
release of sequestered calcium ion into cytosol IEA
Inferred from Electronic Annotation
more info
 
smooth muscle contraction ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal membrane TAS
Traceable Author Statement
more info
 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_016153.1 RefSeqGene

    Range
    5001..46723
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_139075.4NP_620714.2  two pore calcium 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
    UniProtKB/TrEMBL
    Q59G56
    Related
    ENSP00000294309.3, ENST00000294309.8
    Conserved Domains (1) summary
    pfam00520
    Location:468697
    Ion_trans; Ion transport protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

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