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    CLEC1A C-type lectin domain family 1 member A [ Homo sapiens (human) ]

    Gene ID: 51267, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CLEC1Aprovided by HGNC
    Official Full Name
    C-type lectin domain family 1 member Aprovided by HGNC
    Primary source
    HGNC:HGNC:24355
    See related
    Ensembl:ENSG00000150048 MIM:606782; AllianceGenome:HGNC:24355
    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
    CLEC1; CLEC-1
    Summary
    This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signaling, glycoprotein turnover, and roles in inflammation and immune response. The encoded protein may play a role in regulating dendritic cell function. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
    Expression
    Biased expression in placenta (RPKM 18.1), lung (RPKM 3.8) and 10 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLEC1A in Genome Data Viewer
    Location:
    12p13.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (10069554..10098985, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9955966..9985656, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (10222153..10251584, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724020 Neighboring gene C-type lectin domain family 12 member B Neighboring gene C-type lectin domain family 1 member B pseudogene Neighboring gene C-type lectin domain containing 9A Neighboring gene RN7SK pseudogene 161 Neighboring gene uncharacterized LOC105369655 Neighboring gene heterogeneous nuclear ribonucleoprotein A/B pseudogene 1 Neighboring gene C-type lectin domain containing 7A

    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. CLEC-1 Acts as a Negative Regulator of Dectin-1 Induced Host Inflammatory Response Signature in Aspergillus fumigatus Keratitis. Zhu G, et al. Invest Ophthalmol Vis Sci, 2021 May 3. PMID 34043748, Free PMC Article
    2. Dendritic cell immunoreceptors: C-type lectin receptors for pattern-recognition and signaling on antigen-presenting cells. Kanazawa N. J Dermatol Sci, 2007 Feb. PMID 17046204
    3. The human C-type lectin-like receptor CLEC-1 is upregulated by TGF-β and primarily localized in the endoplasmic membrane compartment. Sattler S, et al. Scand J Immunol, 2012 Mar. PMID 22117783
    4. Histidine-Rich Glycoprotein Stimulates Human Neutrophil Phagocytosis and Prolongs Survival through CLEC1A. Takahashi Y, et al. J Immunol, 2021 Feb 15. PMID 33452125, Free PMC Article
    5. Molecular characterization of two novel C-type lectin-like receptors, one of which is selectively expressed in human dendritic cells. Colonna M, et al. Eur J Immunol, 2000 Feb. PMID 10671229

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CLEC-1 Acts as a Negative Regulator of Dectin-1 Induced Host Inflammatory Response Signature in Aspergillus fumigatus Keratitis.
      Title: CLEC-1 Acts as a Negative Regulator of Dectin-1 Induced Host Inflammatory Response Signature in Aspergillus fumigatus Keratitis.
    2. Histidine-Rich Glycoprotein Stimulates Human Neutrophil Phagocytosis and Prolongs Survival through CLEC1A.
      Title: Histidine-Rich Glycoprotein Stimulates Human Neutrophil Phagocytosis and Prolongs Survival through CLEC1A.
    3. Expression of CLEC-1 mRNA was detected in myeloid cells as well as in endothelial cells. CLEC-1 protein displayed N-linked glycosylation and formed dimers.
      Title: The human C-type lectin-like receptor CLEC-1 is upregulated by TGF-β and primarily localized in the endoplasmic membrane compartment.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Aspergillosis, susceptibility to
    MedGen: C3279774 OMIM: 614079 GeneReviews: Not available
    		Compare labs

    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

    • MGC34328

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transmembrane signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    C-type lectin domain family 1 member A
    Names
    C-type lectin-like receptor-1

    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_001297748.2 → NP_001284677.1  C-type lectin domain family 1 member A isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AC024224, AK091989, BC067746
      Consensus CDS
      CCDS73443.1
      UniProtKB/TrEMBL
      B3KRP6, E9PFB4
      Related
      ENSP00000415048.2, ENST00000457018.6
      Conserved Domains (1) summary
      cd03593
      Location:104 → 226
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    2. NM_001297749.2 → NP_001284678.1  C-type lectin domain family 1 member A isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons in the 5' coding region compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC024224, AK300979, AY358587, BC067746
      Consensus CDS
      CCDS76528.1
      UniProtKB/TrEMBL
      B4DV89, E7ESV9
      Related
      ENSP00000417010.2, ENST00000420265.2
      Conserved Domains (1) summary
      cd03593
      Location:45 → 167
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    3. NM_001297750.2 → NP_001284679.1  C-type lectin domain family 1 member A isoform d

      See identical proteins and their annotated locations for NP_001284679.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate exon compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG to encode an isoform (d) that has a shorter N-terminus, compared to isoform a. Variants 4 and 5 encode the same isoform.
      Source sequence(s)
      AC024224, AY358587, BC067746, BX380212
      UniProtKB/TrEMBL
      B4DV89
      Conserved Domains (1) summary
      cd03593
      Location:49 → 171
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    4. NM_001297751.2 → NP_001284680.1  C-type lectin domain family 1 member A isoform d

      See identical proteins and their annotated locations for NP_001284680.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in an internal exon compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG to encode an isoform (d) that has a shorter N-terminus, compared to isoform a. Variants 4 and 5 encode the same isoform.
      Source sequence(s)
      AC024224, AY358587, BC067746, BX339075
      UniProtKB/TrEMBL
      B4DV89
      Conserved Domains (1) summary
      cd03593
      Location:49 → 171
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    5. NM_016511.4 → NP_057595.2  C-type lectin domain family 1 member A isoform a

      See identical proteins and their annotated locations for NP_057595.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC024224, AK075114, BC067746
      Consensus CDS
      CCDS8612.1
      UniProtKB/Swiss-Prot
      Q8IUW7, Q8NC01, Q9NZH3
      UniProtKB/TrEMBL
      A8K6B9
      Related
      ENSP00000326407.4, ENST00000315330.8
      Conserved Domains (1) summary
      cd03593
      Location:137 → 259
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      10069554..10098985 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520687.3 → XP_011518989.1  C-type lectin domain family 1 member A isoform X1

      UniProtKB/TrEMBL
      A8K6B9
      Conserved Domains (1) summary
      cd03593
      Location:164 → 286
      CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      9955966..9985656 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372192.1 → XP_054228167.1  C-type lectin domain family 1 member A isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NC01.2 GenPept UniProtKB/Swiss-Prot:Q8NC01

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