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    MCOLN3 mucolipin TRP cation channel 3 [ Homo sapiens (human) ]

    Gene ID: 55283, updated on 2-Nov-2024

    Summary

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    Official Symbol
    MCOLN3provided by HGNC
    Official Full Name
    mucolipin TRP cation channel 3provided by HGNC
    Primary source
    HGNC:HGNC:13358
    See related
    Ensembl:ENSG00000055732 MIM:607400; AllianceGenome:HGNC:13358
    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
    TRPML3; TRP-ML3
    Summary
    This gene encodes one of members of the mucolipin cation channel proteins. Mutation studies of the highly similar protein in mice have shown that the protein is found in cochlea hair cells, and mutant mice show early-onset hearing loss and balance problems. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
    Expression
    Biased expression in adrenal (RPKM 27.0), skin (RPKM 3.3) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MCOLN3 in Genome Data Viewer
    Location:
    1p22.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (85018082..85048500, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (84858716..84889133, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (85483765..85514183, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene lysophosphatidic acid receptor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1259 Neighboring gene Sharpr-MPRA regulatory region 13288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1260 Neighboring gene mucolipin TRP cation channel 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1027 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:85463659-85464530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1265 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:85527645-85528145 Neighboring gene dynein axonemal intermediate chain 3 Neighboring gene microRNA 4423

    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. A novel mode of TRPML3 regulation by extracytosolic pH absent in the varitint-waddler phenotype. Kim HJ, et al. EMBO J, 2008 Apr 23. PMID 18369318, Free PMC Article
    2. The calcium channel mucolipin-3 is a novel regulator of trafficking along the endosomal pathway. Martina JA, et al. Traffic, 2009 Aug. PMID 19497048, Free PMC Article
    3. The Ca(2+) channel TRPML3 regulates membrane trafficking and autophagy. Kim HJ, et al. Traffic, 2009 Aug. PMID 19522758, Free PMC Article
    4. Palmitoylation controls trafficking of the intracellular Ca(2+) channel MCOLN3/TRPML3 to regulate autophagy. Kim SW, et al. Autophagy, 2019 Feb. PMID 30215288, Free PMC Article
    5. Properties of the TRPML3 channel pore and its stable expansion by the Varitint-Waddler-causing mutation. Kim HJ, et al. J Biol Chem, 2010 May 28. PMID 20378547, Free PMC Article

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. palmitoylation is a prerequisite for the function of MCOLN3/TRPML3 as a Ca(2+) channel in autophagosome formation.
      Title: Palmitoylation controls trafficking of the intracellular Ca(2+) channel MCOLN3/TRPML3 to regulate autophagy.
    2. The work elucidates the molecular architecture and provides insights into how multiple ligands regulate TRPML1 and TRPML3. (Review)
      Title: The regulatory mechanism of mammalian TRPMLs revealed by cryo-EM.
    3. these results suggest that TRPML3 plays a role in autophagosome maturation through the interaction with GATE16, by providing Ca(2+) in the fusion process.
      Title: The Ca2+ channel TRPML3 specifically interacts with the mammalian ATG8 homologue GATE16 to regulate autophagy.
    4. TRPML3 and TRPV5 heteromers could have a biological function
      Title: A novel ion channel formed by interaction of TRPML3 with TRPV5.
    5. Negatively charged amino acids in the extracellular loops of TRPML3 may interfere with the observed sodium inhibition.
      Title: Constitutive activity of TRPML2 and TRPML3 channels versus activation by low extracellular sodium and small molecules.
    6. TRPML 1, 2 and 3 assemblies regulated cell viability and starvation-induced autophagy.
      Title: Heteromultimeric TRPML channel assemblies play a crucial role in the regulation of cell viability models and starvation-induced autophagy.
    7. analysis of the TRPML3 channel pore and its stable expansion by the Varitint-Waddler-causing mutation
      Title: Properties of the TRPML3 channel pore and its stable expansion by the Varitint-Waddler-causing mutation.
    8. Data show that TRPMLs form distinct functional channel complexes.
      Title: Functional multimerization of mucolipin channel proteins.
    9. Results show that mucolipin 3 is a novel calcium channel that plays a crucial role in the regulation of cargo trafficking along the endosomal pathway.
      Title: The calcium channel mucolipin-3 is a novel regulator of trafficking along the endosomal pathway.
    10. These findings reveal a prominent role for TRPML3 in regulating endocytosis, membrane trafficking and autophagy, perhaps by controlling the Ca(2+) in the vicinity of cellular organelles that is necessary to regulate these cellular events.
      Title: The Ca(2+) channel TRPML3 regulates membrane trafficking and autophagy.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11006, FLJ36629, MGC71509

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NAADP-sensitive calcium-release channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium channel activity TAS
    Traceable Author Statement
    more info
    		  
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables monoatomic anion channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables potassium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables sodium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    involved_in calcium-mediated signaling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in inner ear auditory receptor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in monoatomic anion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in potassium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in autophagosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    mucolipin-3
    Names
    mucolipin 3
    transient receptor potential channel mucolipin 3

    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_001253693.2 → NP_001240622.1  mucolipin-3 isoform 2

      See identical proteins and their annotated locations for NP_001240622.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AK001868, BP358726, BQ006750, BU634119, BX483450, CB159774, W03483
      Consensus CDS
      CCDS58009.1
      UniProtKB/TrEMBL
      A8K841
      Related
      ENSP00000342698.3, ENST00000341115.8
      Conserved Domains (1) summary
      pfam08016
      Location:319 → 452
      PKD_channel; Polycystin cation channel

    2. NM_018298.11 → NP_060768.8  mucolipin-3 isoform 1

      See identical proteins and their annotated locations for NP_060768.8

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AF475085, BP358726, BQ006750, BU634119, BX647497, CB159774, W03483
      Consensus CDS
      CCDS701.1
      UniProtKB/Swiss-Prot
      Q5T4H5, Q5T4H6, Q8TDD5, Q9NV09
      UniProtKB/TrEMBL
      A8K841
      Related
      ENSP00000359621.1, ENST00000370589.7
      Conserved Domains (1) summary
      pfam08016
      Location:375 → 508
      PKD_channel; Polycystin cation channel

    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
      85018082..85048500 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005271003.2 → XP_005271060.1  mucolipin-3 isoform X2

      See identical proteins and their annotated locations for XP_005271060.1

      UniProtKB/Swiss-Prot
      Q5T4H5, Q5T4H6, Q8TDD5, Q9NV09
      UniProtKB/TrEMBL
      A8K841
      Conserved Domains (1) summary
      pfam08016
      Location:375 → 508
      PKD_channel; Polycystin cation channel

    2. XM_011541740.3 → XP_011540042.1  mucolipin-3 isoform X3

      UniProtKB/TrEMBL
      A8K841
      Conserved Domains (1) summary
      pfam08016
      Location:343 → 476
      PKD_channel; Polycystin cation channel

    3. XM_011541739.3 → XP_011540041.3  mucolipin-3 isoform X1

    4. XM_047424403.1 → XP_047280359.1  mucolipin-3 isoform X5

    5. XM_011541741.3 → XP_011540043.1  mucolipin-3 isoform X4

    6. XM_047424402.1 → XP_047280358.1  mucolipin-3 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      84858716..84889133 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337496.1 → XP_054193471.1  mucolipin-3 isoform X2

      UniProtKB/Swiss-Prot
      Q5T4H5, Q5T4H6, Q8TDD5, Q9NV09

    2. XM_054337497.1 → XP_054193472.1  mucolipin-3 isoform X3

    3. XM_054337495.1 → XP_054193470.1  mucolipin-3 isoform X1

    4. XM_054337500.1 → XP_054193475.1  mucolipin-3 isoform X5

    5. XM_054337499.1 → XP_054193474.1  mucolipin-3 isoform X4

    6. XM_054337498.1 → XP_054193473.1  mucolipin-3 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TDD5.1 GenPept UniProtKB/Swiss-Prot:Q8TDD5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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