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Clec16a C-type lectin domain family 16, member A [ Mus musculus (house mouse) ]

Gene ID: 74374, updated on 5-Mar-2024

Summary

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Official Symbol
Clec16aprovided by MGI
Official Full Name
C-type lectin domain family 16, member Aprovided by MGI
Primary source
MGI:MGI:1921624
See related
Ensembl:ENSMUSG00000068663 AllianceGenome:MGI:1921624
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
curt; mKIAA0350; 4932416N17Rik
Summary
Acts upstream of or within negative regulation of mitophagy; negative regulation of proteasomal ubiquitin-dependent protein catabolic process; and positive regulation of autophagosome maturation. Located in endolysosome membrane. Used to study neurodegenerative disease. Human ortholog(s) of this gene implicated in Addison's disease; multiple sclerosis; rheumatoid arthritis; and type 1 diabetes mellitus. Orthologous to human CLEC16A (C-type lectin domain containing 16A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in cerebellum adult (RPKM 3.2), cortex adult (RPKM 3.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
16 A1; 16 5.68 cM
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (10363173..10562742)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (10545309..10744878)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene class II transactivator Neighboring gene predicted gene, 57630 Neighboring gene STARR-positive B cell enhancer ABC_E5523 Neighboring gene STARR-positive B cell enhancer ABC_E10887 Neighboring gene dexamethasone-induced transcript Neighboring gene STARR-seq mESC enhancer starr_40088 Neighboring gene predicted gene, 52264 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:10666979-10667180 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:10668626-10668834 Neighboring gene predicted gene 15558 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:10690115-10690396 Neighboring gene STARR-seq mESC enhancer starr_40095 Neighboring gene predicted gene, 53935 Neighboring gene STARR-positive B cell enhancer ABC_E3162 Neighboring gene suppressor of cytokine signaling 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The Autoimmunity-Associated Gene CLEC16A Modulates Thymic Epithelial Cell Autophagy and Alters T Cell Selection. Schuster C, et al. Immunity, 2015 May 19. PMID 25979422, Free PMC Article
  2. JAK/STAT inhibitor therapy partially rescues the lipodystrophic autoimmune phenotype in Clec16a KO mice. Pandey R, et al. Sci Rep, 2021 Apr 1. PMID 33795715, Free PMC Article
  3. Long noncoding RNA Malat1 regulates differential activation of macrophages and response to lung injury. Cui H, et al. JCI Insight, 2019 Feb 21. PMID 30676324, Free PMC Article
  4. CLEC16A regulates splenocyte and NK cell function in part through MEK signaling. Pandey R, et al. PLoS One, 2018. PMID 30226884, Free PMC Article
  5. Clec16a is Critical for Autolysosome Function and Purkinje Cell Survival. Redmann V, et al. Sci Rep, 2016 Mar 18. PMID 26987296, Free PMC Article

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Inducible knockout of Clec16a in mice results in sensory neurodegeneration.
    Title: Inducible knockout of Clec16a in mice results in sensory neurodegeneration.
  2. Study found that lncRNA Malat1 expression is distinctly regulated in differentially activated macrophages in that it is upregulated in LPS-treated and downregulated in IL-4-treated cells. Malat1 regulates the expression of Clec16a, which is required for the proinflammatory activation of macrophages. Data demonstrate that Malat1 is involved in pulmonary pathogeneses in association with aberrant macrophage activation.
    Title: Long noncoding RNA Malat1 regulates differential activation of macrophages and response to lung injury.
  3. CLEC16A restrains secretory functions including cytokine release and cytotoxicity, and a delicate balance of CLEC16A is needed for NK cell function and homeostasis.
    Title: The Autoimmune Disorder Susceptibility Gene CLEC16A Restrains NK Cell Function in YTS NK Cell Line and Clec16a Knockout Mice.
  4. regulates splenocyte and NK cell function in part through MEK signaling
    Title: CLEC16A regulates splenocyte and NK cell function in part through MEK signaling.
  5. Study provides evidence that Clec16a plays a key role in the survival of Purkinje cells and in the degradative function or clearance of autolysosomes.
    Title: Clec16a is Critical for Autolysosome Function and Purkinje Cell Survival.
  6. CLEC16A associations in common variable immunodeficiency disorder represent the first robust evidence of non-HLA associations in this immunodeficiency condition.
    Title: Association of CLEC16A with human common variable immunodeficiency disorder and role in murine B cells.
  7. The novel Pdx1-Clec16a-Nrdp1 pathway this study describes provides a genetic basis for the pathogenesis of mitochondrial dysfunction in multiple forms of diabetes.
    Title: Diabetes Susceptibility Genes Pdx1 and Clec16a Function in a Pathway Regulating Mitophagy in β-Cells.
  8. Islets from mice with pancreas-specific deletion of Clec16a have abnormal mitochondria with reduced oxygen consumption and ATP concentration, both of which are required for normal beta cell function, Clec16a controls beta cell function and prevents diabetes by controlling mitophagy.
    Title: The diabetes susceptibility gene Clec16a regulates mitophagy.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Spontaneous (1) 
  • Targeted (1)  1 citation
  • Endonuclease-mediated (3) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0350

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within autophagy IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to starvation ISO
Inferred from Sequence Orthology
more info
  
involved_in endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosome to lysosome transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of autophagosome maturation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within negative regulation of mitophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within negative regulation of proteasomal ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of TORC1 signaling ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within positive regulation of autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of proteasome-mediated ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of autophagosome maturation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
is_active_in endolysosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endolysosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endosome IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with late endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in vesicle ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
protein CLEC16A

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_001204229.1 → NP_001191158.1  protein CLEC16A isoform 2

    See identical proteins and their annotated locations for NP_001191158.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC122352, AC154430, CT010583
    Consensus CDS
    CCDS57018.1
    UniProtKB/TrEMBL
    Z4YLG3
    Related
    ENSMUSP00000123189.2, ENSMUST00000155633.8
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; uncharacterized conserved protein

  2. NM_177562.5 → NP_808230.2  protein CLEC16A isoform 1

    See identical proteins and their annotated locations for NP_808230.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC122352, AK122255, BU700909
    Consensus CDS
    CCDS37253.1
    UniProtKB/Swiss-Prot
    A6X932, B2RSL3, Q3TCF2, Q3U0F5, Q3U2F6, Q80U30, Q8CEQ8
    UniProtKB/TrEMBL
    Z4YLG3
    Related
    ENSMUSP00000065423.8, ENSMUST00000066345.15
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; uncharacterized conserved protein

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    10363173..10562742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006522660.3 → XP_006522723.1  protein CLEC16A isoform X1

    UniProtKB/TrEMBL
    Z4YLG3
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  2. XM_006522662.3 → XP_006522725.1  protein CLEC16A isoform X3

    UniProtKB/TrEMBL
    Z4YLG3
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  3. XM_030249311.1 → XP_030105171.1  protein CLEC16A isoform X4

    UniProtKB/TrEMBL
    Z4YLG3
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  4. XM_006522661.3 → XP_006522724.1  protein CLEC16A isoform X2

    UniProtKB/TrEMBL
    Z4YLG3
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  5. XM_006522663.3 → XP_006522726.1  protein CLEC16A isoform X5

    UniProtKB/TrEMBL
    Z4YLG3
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  6. XM_036160163.1 → XP_036016056.1  protein CLEC16A isoform X6

    UniProtKB/TrEMBL
    Z4YLG3
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  7. XM_036160164.1 → XP_036016057.1  protein CLEC16A isoform X7

    UniProtKB/TrEMBL
    Z4YLG3
    Related
    ENSMUSP00000111493.2, ENSMUST00000115827.8
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  8. XM_036160165.1 → XP_036016058.1  protein CLEC16A isoform X9

    UniProtKB/TrEMBL
    Z4YLG3
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  9. XM_017317148.2 → XP_017172637.1  protein CLEC16A isoform X10

    UniProtKB/TrEMBL
    H7BXB6
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  10. XM_006522665.4 → XP_006522728.1  protein CLEC16A isoform X12

    UniProtKB/TrEMBL
    H7BXB6
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  11. XM_036160166.1 → XP_036016059.1  protein CLEC16A isoform X14

    UniProtKB/TrEMBL
    H7BXB6
    Related
    ENSMUSP00000111494.3, ENSMUST00000115828.9
    Conserved Domains (2) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein
    pfam12485
    Location:373 → 432
    SLY; Lymphocyte signaling adaptor protein

  12. XM_030249313.2 → XP_030105173.1  protein CLEC16A isoform X16

    UniProtKB/TrEMBL
    H7BXB6
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  13. XM_030249312.2 → XP_030105172.1  protein CLEC16A isoform X13

    UniProtKB/TrEMBL
    H7BXB6
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  14. XM_017317149.2 → XP_017172638.1  protein CLEC16A isoform X15

    UniProtKB/TrEMBL
    H7BXB6
    Conserved Domains (1) summary
    pfam09758
    Location:51 → 198
    FPL; Uncharacterized conserved protein

  15. XM_011246027.4 → XP_011244329.1  protein CLEC16A isoform X8

    UniProtKB/TrEMBL
    Z4YLG3
    Conserved Domains (1) summary
    pfam09758
    Location:1 → 60
    FPL; Uncharacterized conserved protein

  16. XM_006522664.4 → XP_006522727.1  protein CLEC16A isoform X11

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80U30.2 GenPept UniProtKB/Swiss-Prot:Q80U30

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