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

Gene ID: 51267, updated on 11-Apr-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
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Genomic context

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Location:
12p13.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (10069554..10098985, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9955966..9985656, complement)
105.20220307 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
  • 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. 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
  3. 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
  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. A novel cluster of lectin-like receptor genes expressed in monocytic, dendritic and endothelial cells maps close to the NK receptor genes in the human NK gene complex. Sobanov Y, et al. Eur J Immunol, 2001 Dec. PMID 11745369

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

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
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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
  
located_in plasma membrane TAS
Traceable Author Statement
more info
 PubMed 

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_2023_10

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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