Seroatlas · Human Serome Atlas

CLEC4M

C-type lectin domain family 4 member M

Also known as: CD209L, CD299, CLC4M_HUMAN, DC-SIGN2, DC-SIGNR, DCSIGNR, HP10347, LSIGN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q9H2X3
Gene
CLEC4M
Ensembl
ENSG00000104938
Chromosome
19
Canonical length
399 aa
Protein class
CD markers, Predicted intracellular proteins, Predicted membrane proteins, Transporters
Secretome location
Intracellular and membrane
Quaternary structure
Homotetramer

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

399 residues, UniProt reviewed canonical sequence.

>Q9H2X3|CLEC4M
     1  MSDSKEPRVQ QLGLLEEDPT TSGIRLFPRD FQFQQIHGHK SSTGCLGHGA LVLQLLSFML
    61  LAGVLVAILV QVSKVPSSLS QEQSEQDAIY QNLTQLKAAV GELSEKSKLQ EIYQELTQLK
   121  AAVGELPEKS KLQEIYQELT RLKAAVGELP EKSKLQEIYQ ELTRLKAAVG ELPEKSKLQE
   181  IYQELTRLKA AVGELPEKSK LQEIYQELTE LKAAVGELPE KSKLQEIYQE LTQLKAAVGE
   241  LPDQSKQQQI YQELTDLKTA FERLCRHCPK DWTFFQGNCY FMSNSQRNWH DSVTACQEVR
   301  AQLVVIKTAE EQNFLQLQTS RSNRFSWMGL SDLNQEGTWQ WVDGSPLSPS FQRYWNSGEP
   361  NNSGNEDCAE FSGSGWNDNR CDVDNYWICK KPAACFRDE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLEC4M can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Cell surface
Secreted
No
Transmembrane segments
1
Mean surface accessibility (rSASA)
0.37
Highest tissue expression
59 nTPM

Expression across tissuesHPA

Tissue

  • liver: 59 nTPM
  • lymph node: 15 nTPM
  • placenta: 6.9 nTPM
  • lung: 3.5 nTPM
  • ovary: 3.2 nTPM
  • testis: 2.3 nTPM

Single-cell type

  • granulosa cells: 27 nCPM
  • sertoli cells: 13 nCPM
  • vascular endothelial cells: 12 nCPM
  • lymphatic endothelial cells: 5.9 nCPM
  • decidual stromal cells: 5.4 nCPM
  • retinal pigment epithelial cells: 4.3 nCPM

Immune cell

  • memory B-cell: 0.1 nTPM
  • basophil: 0 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM
  • intermediate monocyte: 0 nTPM

Brain region

  • medulla oblongata: 2 nTPM
  • midbrain: 1.3 nTPM
  • pons: 1.3 nTPM
  • cerebral cortex: 1 nTPM
  • spinal cord: 0.9 nTPM
  • cerebellum: 0.8 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
1.12
gnomAD pLI
0
gnomAD missense Z
0.92
DepMap mean gene effect
0.16
DepMap dependency class
none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 2% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CLEC4M as an antibody target. Whether an autoantibody or antibody against CLEC4M could matter depends on whether native CLEC4M is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CLEC4M is annotated at the cell surface, where native CLEC4M is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label CLEC4M as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/CLEC4M. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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