NCBI 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].
Protein
Protein (NP_055072)
CLEC4M - DC-SIGNR
C-type lectin domain family 4 member M (CD209 antigen-like protein 1) (DC-SIGN-related protein) (DC-SIGNR) (Dendritic cell-specific ICAM-3-grabbing non-integrin 2) (DC-SIGN2) (Liver/lymph node-specific ICAM-3-grabbing non-integrin) (L-SIGN) (CD antigen CD299)
CLEC4M
C-type lectin domain family 4 member M
CD299
Curated
C-type lectin
CLEC4M
C-type - Type II transmembrane receptors
a/b mixed / C-type lectin-like
Man, GlcNAc / Oligomannose
NP_055072
10332
Q9H2X3
ENSP00000316228.4
Q9H2X3
0.542
10.1038/nsmb784
neXtProt, PFAM, InterPro
Protein sequence and protein families (fasta) (399 amino acids) Download
MSDSKEPRVQQLGLLEEDPTTSGIRLFPRDFQFQQIHGHKSSTGCLGHGALVLQLLSFMLLAGVLVAILVQVSKVPSSLSQEQSEQDAIYQNLTQLKAAVGELSEKSKLQEIYQELTQLKAAVGELPEKSKLQEIYQELTRLKAAVGELPEKSKLQEIYQELTRLKAAVGELPEKSKLQEIYQELTRLKAAVGELPEKSKLQEIYQELTELKAAVGELPEKSKLQEIYQELTQLKAAVGELPDQSKQQQIYQELTDLKTAFERLCRHCPKDWTFFQGNCYFMSNSQRNWHDSVTACQEVRAQLVVIKTAEEQNFLQLQTSRSNRFSWMGLSDLNQEGTWQWVDGSPLSPSFQRYWNSGEPNNSGNEDCAEFSGSGWNDNRCDVDNYWICKKPAACFRDE
Mol* PDB structure viewerUniLectin3D
Structural models
AlphaFold v2: AF-Q9H2X3-F1Download
  Model Confidence:
  •    Very high (pLDDT > 90)
  •    Confident (90 > pLDDT > 70)
  •    Low (70 > pLDDT > 50)
  •    Very low (pLDDT < 50)

  AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

AlphaFold_v2 structural model assessment through SWISS-MODEL tools.

Ligand
Glycan ligands from structural data
bGlcNAc12aMan13(bGlcNAc12aMan16)Man
GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man
1K9J
1K9J
GlyConnect Structures
bGal14(aFuc13)GlcNAc
Gal(b1-4)[Fuc(a1-3)]GlcNAc
1SL6
1SL6
GlyConnect Structures
Expression
Human Protein Atlas
GeneCards
mRNA expression in normal human tissues for CLEC4M Gene
ProteomicsDB
References
NCBI References (10 PubMed Identifiers)
  • Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies. [34464958]
  • CLEC4M overexpression inhibits progression and is associated with a favorable prognosis in hepatocellular carcinoma. [32705212]
  • SARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune Receptors. [32766577]
  • COVID-19, Renin-Angiotensin System and Endothelial Dysfunction. [32660065]
  • DC-SIGN, DC-SIGNR and LSECtin: C-type lectins for infection. [24156700]
  • Homozygous L-SIGN (CLEC4M) plays a protective role in SARS coronavirus infection. [16369534]
  • Extended neck regions stabilize tetramers of the receptors DC-SIGN and DC-SIGNR. [15509576]
  • DC-SIGNR, a DC-SIGN homologue expressed in endothelial cells, binds to human and simian immunodeficiency viruses and activates infection in trans. [11226297]
  • DC-SIGN. a related gene, DC-SIGNR. and CD23 form a cluster on 19p13. [10975799]
  • Selection of cDNAs encoding putative type II membrane proteins on the cell surface from a human full-length cDNA bank. [10072769]
UniProt Main References (21 PubMed Identifiers)
  • Extensive repertoire of membrane-bound and soluble dendritic cell-specific ICAM-3-grabbing nonintegrin 1 (DC-SIGN1) and DC-SIGN2 isoforms. Inter-individual variation in expression of DC-SIGN transcripts. [11337487]
  • A dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN)-related protein is highly expressed on human liver sinusoidal endothelial cells and promotes HIV-1 infection. [11257134]
  • Complete sequencing and characterization of 21,243 full-length human cDNAs. [14702039]
  • The DNA sequence and biology of human chromosome 19. [15057824]
  • The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). [15489334]
  • A novel mechanism of carbohydrate recognition by the C-type lectins DC-SIGN and DC-SIGNR. Subunit organization and binding to multivalent ligands. [11384997]
  • Human cytomegalovirus binding to DC-SIGN is required for dendritic cell infection and target cell trans-infection. [12433371]
  • C-type lectins DC-SIGN and L-SIGN mediate cellular entry by Ebola virus in cis and in trans. [12050398]
  • Differential N-linked glycosylation of human immunodeficiency virus and Ebola virus envelope glycoproteins modulates interactions with DC-SIGN and DC-SIGNR. [12502850]
  • DC-SIGN and DC-SIGNR interact with the glycoprotein of Marburg virus and the S protein of severe acute respiratory syndrome coronavirus. [15479853]
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All isoforms of this gene containing a lectin domain
NP_001138378.1, NP_001138379.1, NP_001138381.1, NP_001138376.1, NP_055072.3, NP_001138377.1, NP_001138382.1, NP_001138380.1, NP_001138383.1
RNA
RNA (Transcript ID: NM_014257.5)
NM_014257.5
C-type lectin domain family 4 member M, transcript variant 1
All isoforms of CLEC4M containing a lectin domain
ENST00000327325.10
25..1224 (or 7763267.. 7768988)
7763243.. 7769605
NCBI Matured mRNA sequence 1841 NTPDownload 
m7G-5')ppp(5'-AACAUCUGGGGACAGCGGGAAAACAUGAGUGACUCCAAGGAACCAAGGGUGCAGCAGCUGGGCCUCCUGGAAGAAGAUCCAACAACCAGUGGCAUCAGACUUUUUCCAAGAGACUUUCAAUUCCAGCAGAUACAUGGCCACAAGAGCUCUACAGGGUGUCUUGGCCAUGGCGCCCUGGUGCUGCAACUCCUCUCCUUCAUGCUCUUGGCUGGGGUCCUGGUGGCCAUCCUUGUCCAAGUGUCCAAGGUCCCCAGCUCCCUAAGUCAGGAACAAUCCGAGCAAGACGCAAUCUACCAGAACCUGACCCAGCUUAAAGCUGCAGUGGGUGAGCUCUCAGAGAAAUCCAAGCUGCAGGAGAUCUACCAGGAGCUGACCCAGCUGAAGGCUGCAGUGGGUGAGUUGCCAGAGAAAUCCAAGCUGCAGGAGAUCUACCAGGAGCUGACCCGGCUGAAGGCUGCAGUGGGUGAGUUGCCAGAGAAAUCCAAGCUGCAGGAGAUCUACCAGGAGCUGACCCGGCUGAAGGCUGCAGUGGGUGAGUUGCCAGAGAAAUCCAAGCUGCAGGAGAUCUACCAGGAGCUGACCCGGCUGAAGGCUGCAGUGGGUGAGUUGCCAGAGAAAUCCAAGCUGCAGGAGAUCUACCAGGAGCUGACGGAGCUGAAGGCUGCAGUGGGUGAGUUGCCAGAGAAAUCCAAGCUGCAGGAGAUCUACCAGGAGCUGACCCAGCUGAAGGCUGCAGUGGGUGAGUUGCCAGACCAGUCCAAGCAGCAGCAAAUCUAUCAAGAACUGACCGAUUUGAAGACUGCAUUUGAACGCCUGUGCCGCCACUGUCCCAAGGACUGGACAUUCUUCCAAGGAAACUGUUACUUCAUGUCUAACUCCCAGCGGAACUGGCACGACUCCGUCACCGCCUGCCAGGAAGUGAGGGCCCAGCUCGUCGUAAUCAAAACUGCUGAGGAGCAGAACUUCCUACAGCUGCAGACUUCCAGGAGUAACCGCUUCUCCUGGAUGGGACUUUCAGACCUAAAUCAGGAAGGCACGUGGCAAUGGGUGGACGGCUCACCUCUGUCACCCAGCUUCCAGCGGUACUGGAACAGUGGAGAACCCAACAAUAGCGGGAAUGAAGACUGUGCGGAAUUUAGUGGCAGUGGCUGGAACGACAAUCGAUGUGACGUUGACAAUUACUGGAUCUGCAAAAAGCCCGCAGCCUGCUUCAGAGACGAAUAGUUGUUUCCCUGCUAGCCUCAGCCUCCAUUGUGGUAUAGCAGAACUUCACCCACUUGUAAGCCAGCGCUUCUUCUCUCCAUCCUUGGACCUUCACAAAUGCCCUGAGACGGUUCUCUGUUCGAUUUUUCAUCCCCUAUGAACCUGGGUCUUAUUCUGUCCUUCUGAUGCCUCCAAGUUUCCCUGGUGUAGAGCUUGUGUUCUUGGCCCAUCCUUGGAGCUUUAUAAGUGACCUGAGUGGGAUGCAUUUAGGGGGCGGGCUUGGUAUGUUGUAUGAAUCCACUCUCUGUUCCUUUUGGAGAUUAGACUAUUUGGAUUCAUGUGUAGCUGCCCUGUCCCCUGGGGCUUUAUCUCAUCCAUGCAAACUACCAUCUGCUCAACUUCCAGCUACACCCCGUGCACCCUUUUGACUGGGGACUUGCUGGUUGAAGGAGCUCAUCUUGCAGGCUGGAAGCACCAGGGAAUUAAUUCCCCCAGUCAACCAAUGGCAUCCAGAGAGGGCAUGGAGGCUCCAUACAACCUCUUCCACCCCCACAUCUUUCUUUGUCCUAUACAUGUCUUCCAUUUGGCUGUUUCUGAGUUGUAGCCUUUAUAAUAAAGUGGUAAAUGUUGUAACUGCA-3'- Poly-A tail
  • Coding region
NCBI Matured mRNA sequence viewer
;
More about the NCBI sViewer.
DNA
DNA (Gene ID: 10332)
CLEC4M
C-type lectin domain family 4 member M
NC_000019.10
19  7763267.. 7768988
7763267.. 7768988
strand +
CCDS12187.1
MGI:1916415;MGI:1917442
ClinVar, dbVar
ENSG00000104938
HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2
uc010dvt.3
INSDC: AB015629
13523
605872
OTTHUMG00000182432
ENA, DDBJ, Monarch
CD299
NCBI CDS Gene viewer
More about the NCBI sViewer.
NCBI CDS gene sequence (1200 bp)
5'-ATGAGTGACTCCAAGGAACCAAGGGTGCAGCAGCTGGGCCTCCTGGAAGAAGATCCAACAACCAGTGGCATCAGACTTTTTCCAAGAGACTTTCAATTCCAGCAGATACATGGCCACAAGAGCTCTACAGGGTGTCTTGGCCATGGCGCCCTGGTGCTGCAACTCCTCTCCTTCATGCTCTTGGCTGGGGTCCTGGTGGCCATCCTTGTCCAAGTGTCCAAGGTCCCCAGCTCCCTAAGTCAGGAACAATCCGAGCAAGACGCAATCTACCAGAACCTGACCCAGCTTAAAGCTGCAGTGGGTGAGCTCTCAGAGAAATCCAAGCTGCAGGAGATCTACCAGGAGCTGACCCAGCTGAAGGCTGCAGTGGGTGAGTTGCCAGAGAAATCCAAGCTGCAGGAGATCTACCAGGAGCTGACCCGGCTGAAGGCTGCAGTGGGTGAGTTGCCAGAGAAATCCAAGCTGCAGGAGATCTACCAGGAGCTGACCCGGCTGAAGGCTGCAGTGGGTGAGTTGCCAGAGAAATCCAAGCTGCAGGAGATCTACCAGGAGCTGACCCGGCTGAAGGCTGCAGTGGGTGAGTTGCCAGAGAAATCCAAGCTGCAGGAGATCTACCAGGAGCTGACGGAGCTGAAGGCTGCAGTGGGTGAGTTGCCAGAGAAATCCAAGCTGCAGGAGATCTACCAGGAGCTGACCCAGCTGAAGGCTGCAGTGGGTGAGTTGCCAGACCAGTCCAAGCAGCAGCAAATCTATCAAGAACTGACCGATTTGAAGACTGCATTTGAACGCCTGTGCCGCCACTGTCCCAAGGACTGGACATTCTTCCAAGGAAACTGTTACTTCATGTCTAACTCCCAGCGGAACTGGCACGACTCCGTCACCGCCTGCCAGGAAGTGAGGGCCCAGCTCGTCGTAATCAAAACTGCTGAGGAGCAGAACTTCCTACAGCTGCAGACTTCCAGGAGTAACCGCTTCTCCTGGATGGGACTTTCAGACCTAAATCAGGAAGGCACGTGGCAATGGGTGGACGGCTCACCTCTGTCACCCAGCTTCCAGCGGTACTGGAACAGTGGAGAACCCAACAATAGCGGGAATGAAGACTGTGCGGAATTTAGTGGCAGTGGCTGGAACGACAATCGATGTGACGTTGACAATTACTGGATCTGCAAAAAGCCCGCAGCCTGCTTCAGAGACGAATAG-3'
NCBI CDS gene sequence with introns (location: 7763267.. 7768988) (5722 bp)Download
NCBI Gene Viewer (CDS + introns)
NCBI CDS gene sequence with introns, 5'UTR and 3'UTR (location: 7763243.. 7769605) (6363 bp)Download
NCBI Gene Viewer (CDS + introns + Untranslated regions)
NCBI gene sequence (location: [7763243 - 1000].. 7769605) (7363 bp)Download
NCBI Gene Viewer (CDS + introns + Untranslated regions + 1000 dNTP to potentially reach the promotor)
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