Human Gene CLEC4M (ENST00000327325.10) from GENCODE V50

Description: C-type lectin domain family 4 member M, transcript variant 4 (from RefSeq NR_026707.2)
Gencode Transcript: ENST00000327325.10
Gencode Gene: ENSG00000104938.20
Transcript (Including UTRs)
Position: hg38 chr19:7,763,243-7,769,605 Size: 6,363 Total Exon Count: 7 Strand: +
Coding Region
Position: hg38 chr19:7,763,267-7,768,988 Size: 5,722 Coding Exon Count: 7

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Other Names	Methods

Data last updated at UCSC: 2026-07-12 09:30:09

Sequence and Links to Tools and Databases

Genomic Sequence (chr19:7,763,243-7,769,605)			mRNA (may differ from genome)		Protein (399 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	Gencode	GeneCards
HGNC	Lynx	Malacards	MGI	myGene2	OMIM
PubMed	UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: CLC4M_HUMAN DESCRIPTION: RecName: Full=C-type lectin domain family 4 member M; AltName: Full=CD209 antigen-like protein 1; AltName: Full=DC-SIGN-related protein; Short=DC-SIGNR; AltName: Full=Dendritic cell-specific ICAM-3-grabbing non-integrin 2; Short=DC-SIGN2; AltName: Full=Liver/lymph node-specific ICAM-3-grabbing non-integrin; Short=L-SIGN; AltName: CD_antigen=CD299; FUNCTION: Probable pathogen-recognition receptor involved in peripheral immune surveillance in liver. May mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, HCV E2, and human SARS coronavirus protein S. Is a receptor for ICAM3, probably by binding to mannose-like carbohydrates. Is presumably a coreceptor for the SARS coronavirus. SUBUNIT: Homotetramer. Binds to many viral surface glycoproteins such as HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, HCV E2, and human SARS coronavirus S protein. SUBCELLULAR LOCATION: Isoform 1: Cell membrane; Single-pass type II membrane protein (Potential). SUBCELLULAR LOCATION: Isoform 2: Cell membrane; Single-pass type II membrane protein (Potential). SUBCELLULAR LOCATION: Isoform 3: Cell membrane; Single-pass type II membrane protein (Potential). SUBCELLULAR LOCATION: Isoform 5: Secreted (Potential). SUBCELLULAR LOCATION: Isoform 6: Secreted (Potential). SUBCELLULAR LOCATION: Isoform 7: Secreted (Potential). SUBCELLULAR LOCATION: Isoform 10: Secreted (Potential). TISSUE SPECIFICITY: Predominantly highly expressed in liver sinusoidal endothelial cells and in lymph node. Found in placental endothelium but not in macrophages. Expressed in type II alveolar cells and lung endothelial cells. DOMAIN: The tandem repeat domain, also called neck domain, mediates oligomerization. POLYMORPHISM: The number of repeats in the tandem repeat domain is shown to vary between 3 and 9 per allele thus contributing to a further variability in addition to alternative splicing. The shown 7 repeat-containing form has been shown to be the most frequent one (53.9%) in a study with 350 Caucasian individuals. MISCELLANEOUS: In vitro, is a receptor for HIV-1 and transmits HIV-1 to permissive T-cells. SIMILARITY: Contains 1 C-type lectin domain. SEQUENCE CAUTION: Sequence=AAR04559.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding; Note=DC-SIGNR; URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_00122";

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: CLEC4M Diseases sorted by gene-association score: japanese encephalitis (26), severe acute respiratory syndrome (18), west nile virus (17), encephalitis (13), hepatitis c virus (12), hepatitis c (7), hiv-1 (4), viral infectious disease (2)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D019256 Cadmium Chloride D004958 Estradiol D013749 Tetrachlorodibenzodioxin

RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 14.88 RPKM in Liver Total median expression: 23.47 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-3.00	24	-0.125	Picture	PostScript	Text
3' UTR	-184.40	617	-0.299	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR001304 - C-type_lectin
IPR016186 - C-type_lectin-like
IPR018378 - C-type_lectin_CS
IPR016187 - C-type_lectin_fold

Pfam Domains:
PF00059 - Lectin C-type domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1K9J - X-ray MuPIT

1SL6 - X-ray MuPIT

1XAR - X-ray MuPIT

1XPH - X-ray MuPIT

1Z0Y - Model

3JQH - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q9H2X3


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
Genome Browser	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details
Gene Sorter
MGI
Protein Sequence
Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0001618 virus receptor activity GO:0005537 mannose binding GO:0030246 carbohydrate binding GO:0030369 ICAM-3 receptor activity GO:0038023 signaling receptor activity GO:0042605 peptide antigen binding GO:0046790 virion binding GO:0046872 metal ion binding GO:0048306 calcium-dependent protein binding Biological Process: GO:0002250 adaptive immune response GO:0002376 immune system process GO:0006897 endocytosis GO:0007159 leukocyte cell-cell adhesion GO:0009988 cell-cell recognition GO:0016032 viral process GO:0019048 modulation by virus of host morphology or physiology GO:0019062 virion attachment to host cell GO:0019079 viral genome replication GO:0019882 antigen processing and presentation GO:0035556 intracellular signal transduction GO:0045087 innate immune response GO:0046718 viral entry into host cell GO:0046968 peptide antigen transport GO:0075733 intracellular transport of virus Cellular Component: GO:0005576 extracellular region GO:0005737 cytoplasm GO:0005886 plasma membrane GO:0005887 integral component of plasma membrane GO:0016020 membrane GO:0016021 integral component of membrane GO:0043657 host cell

Descriptions from all associated GenBank mRNAs


	AK292278 - Homo sapiens cDNA FLJ77783 complete cds, highly similar to Homo sapiens CD209 antigen-like (CD209L), mRNA. BC038851 - Homo sapiens C-type lectin domain family 4, member M, mRNA (cDNA clone MGC:47866 IMAGE:5166966), complete cds. AF290887 - Homo sapiens L-SIGN mRNA, complete cds. AK314704 - Homo sapiens cDNA, FLJ95558. AK304499 - Homo sapiens cDNA FLJ52840 complete cds, highly similar to C-type lectin domain family 4 member M. JD231731 - Sequence 212755 from Patent EP1572962. JD206134 - Sequence 187158 from Patent EP1572962. AB015629 - Homo sapiens mRNA for type II membrane protein similar to HIV gp120-binding C-type lectin, complete cds, clone:HP01347. AF245219 - Homo sapiens probable mannose binding C-type lectin DC-SIGNR mRNA, complete cds. AK298084 - Homo sapiens cDNA FLJ55003 complete cds, highly similar to Homo sapiens C-type lectin domain family 4, member M (CLEC4M), transcript variant 6, mRNA. AK023750 - Homo sapiens cDNA FLJ13688 fis, clone PLACE2000062, highly similar to Homo sapiens mRNA for type II membrane protein. BC110614 - Homo sapiens C-type lectin domain family 4, member M, mRNA (cDNA clone MGC:129964 IMAGE:40032453), complete cds. KJ902090 - Synthetic construct Homo sapiens clone ccsbBroadEn_11484 CLEC4M gene, encodes complete protein. DQ893779 - Synthetic construct Homo sapiens clone IMAGE:100008239; FLH167490.01L; RZPDo839B0589D C-type lectin domain family 4, member M (CLEC4M) gene, encodes complete protein. KJ898195 - Synthetic construct Homo sapiens clone ccsbBroadEn_07589 CLEC4M gene, encodes complete protein. AY343913 - Homo sapiens L-SIGN variant (CD209L) mRNA, complete cds. AY042234 - Homo sapiens mDC-SIGN2 type I isoform (CD209L) mRNA, complete cds, alternatively spliced. AY042235 - Homo sapiens mDC-SIGN2 type III isoform (CD209L) mRNA, complete cds, alternatively spliced. AY042236 - Homo sapiens mDC-SIGN2 type IV isoform (CD209L) mRNA, complete cds, alternatively spliced. AY042237 - Homo sapiens mDC-SIGN2 type VI isoform (CD209L) mRNA, complete cds, alternatively spliced. AY042238 - Homo sapiens sDC-SIGN2 type I isoform (CD209L) mRNA, complete cds, alternatively spliced. AY042239 - Homo sapiens sDC-SIGN2 type II isoform (CD209L) mRNA, complete cds, alternatively spliced. AY042240 - Homo sapiens sDC-SIGN2 type III isoform (CD209L) mRNA, complete cds, alternatively spliced. JD555088 - Sequence 536112 from Patent EP1572962. JD462147 - Sequence 443171 from Patent EP1572962. JD094413 - Sequence 75437 from Patent EP1572962. JD249117 - Sequence 230141 from Patent EP1572962. JD276142 - Sequence 257166 from Patent EP1572962. JD251588 - Sequence 232612 from Patent EP1572962. JD249348 - Sequence 230372 from Patent EP1572962. JD535830 - Sequence 516854 from Patent EP1572962. JD111353 - Sequence 92377 from Patent EP1572962. JD516861 - Sequence 497885 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: A6NKI4, A8K8B3, CD209L, CD209L1, CD299, CLC4M_HUMAN, ENST00000327325.1, ENST00000327325.2, ENST00000327325.3, ENST00000327325.4, ENST00000327325.5, ENST00000327325.6, ENST00000327325.7, ENST00000327325.8, ENST00000327325.9, NR_026707, Q69F40, Q969M4, Q96QP3, Q96QP4, Q96QP5, Q96QP6, Q9BXS3, Q9H2Q9, Q9H2X3, Q9H8F0, Q9Y2A8, uc010dvt.1, uc010dvt.2, uc010dvt.3, uc010dvt.4 UCSC ID: ENST00000327325.10 RefSeq Accession: NM_014257.5 Protein: Q9H2X3 (aka CLC4M_HUMAN) CCDS: CCDS12187.1

Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.

GNF Expression Atlas 2 Data from U133A and GNF1H Chips