Format

Send to:

Choose Destination
    • Showing Current items.

    CLEC4M C-type lectin domain family 4 member M [ Homo sapiens (human) ]

    Gene ID: 10332, updated on 22-Jun-2021

    Summary

    Official Symbol
    CLEC4Mprovided by HGNC
    Official Full Name
    C-type lectin domain family 4 member Mprovided by HGNC
    Primary source
    HGNC:HGNC:13523
    See related
    Ensembl:ENSG00000104938 MIM:605872
    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
    CD299; LSIGN; CD209L; L-SIGN; DCSIGNR; HP10347; DC-SIGN2; DC-SIGNR
    Summary
    This gene encodes a C-type lectin that functions in cell adhesion and pathogen recognition. This receptor recognizes a wide range of evolutionarily divergent pathogens with a large impact on public health, including tuberculosis mycobacteria, and viruses including Ebola, hepatitis C, HIV-1, influenza A, West Nile virus and the SARS-CoV acute respiratory syndrome coronavirus. The protein is organized into four distinct domains: a C-terminal carbohydrate recognition domain, a flexible tandem-repeat neck domain of variable length, a transmembrane region and an N-terminal cytoplasmic domain involved in internalization. This gene is closely related in terms of both sequence and function to a neighboring gene, CD209 (Gene ID: 30835), also known as DC-SIGN. The two genes differ in viral recognition and expression patterns, with this gene showing high expression in endothelial cells of the liver, lymph node and placenta. Polymorphisms in the tandem repeat neck domain are associated with resistance to SARS infection. [provided by RefSeq, May 2020]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is relevant for COVID-19 prognosis.
    Expression
    Biased expression in liver (RPKM 15.4), lymph node (RPKM 9.8) and 3 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CLEC4M in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (7763243..7769605)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (7828129..7834491)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CD209 promoter region Neighboring gene Sharpr-MPRA regulatory region 7484 Neighboring gene ribosomal protein L21 pseudogene 129 Neighboring gene CLEC4M promoter region Neighboring gene uncharacterized LOC105372263 Neighboring gene C-type lectin domain family 4 member G pseudogene 1

    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 Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Crystal structures of carbohydrate-recognition domains of DC-SIGN and of DC-SIGNR in combination with binding studies reveal that these receptors selectively recognize endogenous high-mannose oligosaccharides of HIV-1 gp120 PubMed
    env HIV-1 gp120 binds to a membrane-associated mannose-binding lectin in a CD4-independent manner PubMed
    env L-SIGN behaves similarly to DC-SIGN in that it has a high affinity for ICAM-3, captures HIV-1 through gp120 binding, and enhances HIV-1 infection of T cells in trans PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC47866, MGC129964

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ICAM-3 receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables calcium-dependent protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables carbohydrate binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables mannose binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables peptide antigen binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables virion binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables virus receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables virus receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in antigen processing and presentation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cell-cell recognition TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in intracellular transport of virus TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in leukocyte cell-cell adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in peptide antigen transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in viral entry into host cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in viral genome replication NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in virion attachment to host cell TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in host cell IEA
    Inferred from Electronic Annotation
    more info
     
    located_in integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    C-type lectin domain family 4 member M
    Names
    CD209 antigen-like protein 1
    CD299 antigen
    DC-SIGN-related protein
    dendritic cell-specific ICAM-3-grabbing non-integrin 2
    liver/lymph node-specific ICAM-3 grabbing non-integrin
    mannose binding C-type lectin DC-SIGNR

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_029190.1 RefSeqGene

      Range
      5095..11457
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001144904.2NP_001138376.1  C-type lectin domain family 4 member M isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon and uses an alternative splice site in the coding region and maintains the reading frame. This results in a shorter protein (isoform 2) compared to isoform 1. This isoform (2) has 6.5 repeats in the neck domain.
      Source sequence(s)
      AC008812, AK304499, BQ008265
      UniProtKB/TrEMBL
      B4E2Z5, H7BXU4
      Related
      ENSP00000377680.3, ENST00000394122.7
      Conserved Domains (1) summary
      cd03590
      Location:217340
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
    2. NM_001144905.2NP_001138377.1  C-type lectin domain family 4 member M isoform 12

      Status: REVIEWED

      Description
      Transcript Variant: This variant (12) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 12, which is shorter than isoform 1. The encoded isoform (12) has 6.5 repeats in the neck domain.
      Source sequence(s)
      AC008812, AK314704, BC038851
      UniProtKB/Swiss-Prot
      Q9H2X3
      Conserved Domains (1) summary
      cd03590
      Location:244367
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
    3. NM_001144906.2NP_001138378.1  C-type lectin domain family 4 member M isoform 7

      See identical proteins and their annotated locations for NP_001138378.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an exon and uses an alternate in-frame splice site in the coding region compared to variant 1. This results in a shorter protein (isoform 7) compared to isoform 1. The encoded isoform (7) lacks a transmembrane domain and has 2.5 repeats in the neck domain.
      Source sequence(s)
      AC008812, AY042240, BC038851, DB048428
      Consensus CDS
      CCDS59347.1
      UniProtKB/Swiss-Prot
      Q9H2X3
      Conserved Domains (1) summary
      cd03590
      Location:132255
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
    4. NM_001144907.2NP_001138379.1  C-type lectin domain family 4 member M isoform 11

      See identical proteins and their annotated locations for NP_001138379.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 11) has a distinct C-terminus and is shorter than isoform 1. The encoded isoform (11) lacks a transmembrane domain and has 5.5 repeats in the neck domain.
      Source sequence(s)
      AY042238, BC038851, DB048428
      UniProtKB/Swiss-Prot
      Q9H2X3
      Conserved Domains (2) summary
      cd03590
      Location:201324
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      cl01483
      Location:89197
      Com_YlbF; Control of competence regulator ComK, YlbF/YmcA
    5. NM_001144908.2NP_001138380.1  C-type lectin domain family 4 member M isoform 10

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 10) has a distinct C-terminus and is shorter than isoform 1. The encoded isoform (10) has 3.5 repeats in the neck domain.
      Source sequence(s)
      AC008812, AY042237, BC038851, DB048428
      Consensus CDS
      CCDS59346.1
      UniProtKB/Swiss-Prot
      Q9H2X3
      Conserved Domains (2) summary
      pfam05816
      Location:83172
      TelA; Toxic anion resistance protein (TelA)
      cl02432
      Location:176220
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    6. NM_001144909.2NP_001138381.1  C-type lectin domain family 4 member M isoform 9

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter protein (isoform 9) compared to isoform 1. The encoded isoform (9) has 5.5 repeats in the neck domain.
      Source sequence(s)
      AC008812, AY343913, BC038851, DB048428
      UniProtKB/Swiss-Prot
      Q9H2X3
      Conserved Domains (2) summary
      cd03590
      Location:222345
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      cl01234
      Location:60196
      PilO; Pilus assembly protein, PilO
    7. NM_001144910.2NP_001138382.1  C-type lectin domain family 4 member M isoform 8

      See identical proteins and their annotated locations for NP_001138382.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter protein (isoform 8) compared to isoform 1. The encoded isoform (8) has 6.5 repeats in the neck domain.
      Source sequence(s)
      AF290887, BC038851
      UniProtKB/Swiss-Prot
      Q9H2X3
      Conserved Domains (1) summary
      cd03590
      Location:245368
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
    8. NM_001144911.2NP_001138383.1  C-type lectin domain family 4 member M isoform 3

      See identical proteins and their annotated locations for NP_001138383.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AB015629, BC038851
      Consensus CDS
      CCDS59348.1
      UniProtKB/Swiss-Prot
      Q9H2X3
      Related
      ENSP00000471125.1, ENST00000596363.5
      Conserved Domains (1) summary
      cl02432
      Location:240284
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    9. NM_014257.5NP_055072.3  C-type lectin domain family 4 member M isoform 1

      See identical proteins and their annotated locations for NP_055072.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC038851
      Consensus CDS
      CCDS12187.1
      UniProtKB/Swiss-Prot
      Q9H2X3
      Related
      ENSP00000316228.4, ENST00000327325.10
      Conserved Domains (2) summary
      cd03590
      Location:268391
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      cl19219
      Location:140251
      DUF342; Protein of unknown function (DUF342)

    RNA

    1. NR_026707.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences in the coding region, compared to variant 1. This variant 4 replaces NM_214677 and is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA431250, AY042235, BC038851, BX102225, DB048428
    2. NR_026708.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has multiple differences in the coding region, compared to variant 1. This variant 5 replaces NM_214678 and is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA431250, AY042236, BC038851, BX102225, DB048428
    3. NR_026709.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) has multiple differences in the coding region, compared to variant 1. This variant 6 replaces NM_214679 and is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA431250, AC008812, AY042239, BC038851, BX102225

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

      Range
      7763243..7769605
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_214675.1: Suppressed sequence

      Description
      NM_214675.1: This RefSeq was permanently suppressed because it is redundant.
    2. NM_214676.1: Suppressed sequence

      Description
      NM_214676.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Support Center