Format

Send to:

Choose Destination

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