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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

CLEC4M Gene

protein-coding GIFtS: 62
GCID: GC19P007828

C-type lectin domain family 4, member M

(Previous name: CD299 antigen )
(Previous symbols: CD209L, CD299)

Explore 15 diseases affiliated with
CLEC4M via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
C-Type Lectin Domain Family 4, Member M¹ ²		Dendritic Cell-Specific ICAM-3-Grabbing Non-Integrin 2² ³
CD209L¹ ² ³ ⁵		Liver/Lymph Node-Specific ICAM-3-Grabbing Non-Integrin² ³
CD299¹ ² ³		L-SIGN² ³
DC-SIGN2¹ ² ³		CD209 Antigen-Like Protein 1² ³
DC-SIGNR¹ ² ³		DC-SIGN-Related Protein² ³
CD299 Antigen¹ ² ³		C-Type Lectin Domain Family 4 Member M²
DCSIGNR¹ ² ⁵		Liver/Lymph Node-Specific ICAM-3 Grabbing Non-Integrin²
LSIGN¹ ² ⁵		Mannose Binding C-Type Lectin DC-SIGNR²
HP10347¹ ²		CD209L1³

External Ids:	HGNC: 13523¹	Entrez Gene: 10332²	Ensembl: ENSG00000104938⁷	OMIM: 605872⁵	UniProtKB: Q9H2X3³

ORGUL members:
	NONCODE:n407239

Export aliases for CLEC4M gene to outside databases

Previous GC identifers: GC19P007735 GC19P007498

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CLEC4M:

This gene encodes a transmembrane receptor and is often referred to as L-SIGN because of its expression in the

endothelial cells of the lymph nodes and liver. The encoded protein is involved in the innate immune system and

recognizes numerous evolutionarily divergent pathogens ranging from parasites to viruses, with a large impact on

public health. The protein is organized into three distinct domains: an N-terminal transmembrane domain, a

tandem-repeat neck domain and C-type lectin carbohydrate recognition domain. The extracellular region consisting of

the C-type lectin and neck domains has a dual function as a pathogen recognition receptor and a cell adhesion receptor

by binding carbohydrate ligands on the surface of microbes and endogenous cells. The neck region is important for

homo-oligomerization which allows the receptor to bind multivalent ligands with high avidity. Variations in the number

of 23 amino acid repeats in the neck domain of this protein are common and have a significant impact on ligand binding

ability. This gene is closely related in terms of both sequence and function to a neighboring gene (GeneID 30835;

often referred to as DC-SIGN or CD209). DC-SIGN and L-SIGN differ in their ligand-binding properties and distribution.

Alternative splicing results in multiple variants.(provided by RefSeq, Feb 2009)

UniProtKB/Swiss-Prot: CLC4M_HUMAN, Q9H2X3

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

Gene Wiki entry for CLEC4M

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000019.9 NC_018930.1 NT_077812.2

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the CLEC4M gene promoter:
ISGF-3 RP58 NRSF form 1 Brachyury NRSF form 2 Evi-1 ARP-1 FOXO1a c-Myb FOXO1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: CLEC4M promoter sequence

Search SABiosciences Chromatin IP Primers for CLEC4M

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLEC4M

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13 Ensembl cytogenetic band: 19p13.2 HGNC cytogenetic band: 19p13

CLEC4M Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC4M gene location

GeneLoc information about chromosome 19 GeneLoc Exon Structure

GeneLoc location for GC19P007828: view genomic region (about GC identifiers)

Start:	7,828,035 bp from pter	End:	7,834,491 bp from pter
Size:	6,457 bases	Orientation:	plus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CLC4M_HUMAN, Q9H2X3 (See protein sequence)

Recommended Name: C-type lectin domain family 4 member M

Size: 399 amino acids; 45350 Da

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)

Miscellaneous: In vitro, is a receptor for HIV-1 and transmits HIV-1 to permissive T-cells

Sequence caution: Sequence=AAR04559.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;

6 PDB 3D structures from and Proteopedia for CLEC4M:

1K9J (3D)

1SL6 (3D)

1XAR (3D)

1XPH (3D)

1Z0Y (3D)

3JQH (3D)

Secondary accessions: A6NKI4 A8K8B3 Q69F40 Q969M4 Q96QP3 Q96QP4 Q96QP5 Q96QP6 Q9BXS3 Q9H2Q9 Q9H8F0

Q9Y2A8

Alternative splicing: 10 isoforms: Q9H2X3-1 Q9H2X3-2 Q9H2X3-3 Q9H2X3-4 Q9H2X3-5 Q9H2X3-6 Q9H2X3-7 Q9H2X3-8

Q9H2X3-9 Q9H2X3-10 (May be due to intron retention)

Explore the universe of human proteins at neXtProt for CLEC4M: NX_Q9H2X3

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9H2X3

CLEC4M Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (9 alternative transcripts):

NP_001138376.1 NP_001138377.1 NP_001138378.1 NP_001138379.1 NP_001138380.1 NP_001138381.1 NP_001138382.1 NP_001138383.1

NP_055072.3

ENSEMBL proteins:

ENSP00000316228 ENSP00000377680 ENSP00000248228 ENSP00000335228 ENSP00000351954

ENSP00000349924

Human Recombinant Protein Products:

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	R&D Systems Recombinant & Natural Proteins for CLEC4M (DC-SIGNR/CD299)
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	OriGene Purified Protein: CLEC4M OriGene Protein Over-expression Lysate (see all 2): CLEC4M OriGene Custom Protein Services for CLEC4M
	GenScript Custom Purified and Recombinant Proteins Services for CLEC4M
	Novus Biologicals CLEC4M Protein Novus Biologicals CLEC4M Lysates
	Sino Biological Recombinant Protein for CLEC4M
	Browse ProSpec Recombinant Proteins
	Uscn Proteins for CLEC4M

Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	IEA	--
GO:0005622	intracellular	--	--
GO:0005737	cytoplasm	NAS	11337487
GO:0005887	integral to plasma membrane	TAS	10072769
GO:0016020	membrane	TAS	11337487

CLEC4M for ontologies About GeneDecksing

CLEC4M Antibody Products:

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	R&D Systems Antibodies for CLEC4M (DC-SIGNR/CD299)
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	GenScript Custom Superior Antibodies Services for CLEC4M
	Novus Biologicals CLEC4M Antibodies
	Search for Antibodies for CLEC4M at Abcam
	Uscn Antibodies for CLEC4M
	Search ThermoFisher Antibodies for CLEC4M

Assay Products for CLEC4M:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for CLEC4M
	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for CLEC4M

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

CLEC4M for domains About GeneDecksing

4 InterPro domains/families:

IPR016187 C-type_lectin_fold

IPR018378 C-type_lectin_CS

IPR016186 C-type_lectin-like

IPR001304 C-type_lectin

Graphical View of Domain Structure for InterPro Entry Q9H2X3

ProtoNet protein and cluster: Q9H2X3

1 Blocks protein family: IPB002353 Type II antifreeze protein signature

UniProtKB/Swiss-Prot: CLC4M_HUMAN, Q9H2X3

Domain: The tandem repeat domain, also called neck domain, mediates oligomerization

Similarity: Contains 1 C-type lectin domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: CLC4M_HUMAN, Q9H2X3

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

miRNA Products:		Browse 3'-UTR reporter clones for miRNA target validation Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CLEC4M
		Search QIAGEN for miScript miRNA Assays for microRNAs that regulate CLEC4M
		SwitchGear 3'UTR luciferase reporter plasmid: CLEC4M 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CLEC4M (see all 7) OriGene shRNA RFP: CLEC4M OriGene siRNA: CLEC4M
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Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for CLEC4M

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
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		GenScript: all cDNA clones in your preferred vector (see all 9): CLEC4M (NM_014257)
		Sino Biological Human cDNA Clone for CLEC4M
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		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLEC4M

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for CLEC4M
		Search LifeMap BioReagents cell lines for CLEC4M

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC4M

Gene Ontology (GO): 5/7 molecular function terms (GO ID links to tree view) (see all 7): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004872	receptor activity	NAS	11257134
GO:0005537	mannose binding	IEA	--
GO:0030246	carbohydrate binding	NAS	11337487
GO:0030369	ICAM-3 receptor activity	NAS	11257134
GO:0042605	peptide antigen binding	NAS	11337487

CLEC4M for ontologies           About GeneDecksing

Animal Models:
     Mouse knock-outs for CLEC4M: Cd209d^tm1Psob Cd209d^tm1.2Olne
     3 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Cd209d):

homeostasis/metabolism

immune system

no phenotypic analysis

CLEC4M for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Measles

Measles

1.00

Tuberculosis

Tuberculosis

1.00

Phagosome

Phagosome

1.00

Pathway sources
See GeneCards unified pathways
Show all pathways

3 Kegg Pathways (Kegg details for CLEC4M):

	Phagosome
	Tuberculosis
	Measles

CLEC4M for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for CLEC4M

STRING Interaction Network Preview (showing 5 interactants - click image to see 15)

5/17 Interacting proteins for CLEC4M (Q9H2X3^{2, 3} ENSP00000316228⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 17)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
CEACAM1	P13688²^,³, ENSP00000161559⁴	MINT-72826 MINT-72821 I2D: score=1 STRING: ENSP00000161559
ITGAM	P11215²^,³, ENSP00000287497⁴	MINT-72825 MINT-72823 I2D: score=1 STRING: ENSP00000287497
CD209	Q9NNX6³, ENSP00000315477⁴	I2D: score=1 STRING: ENSP00000315477
AP2M1	Q96CW1³, ENSP00000292807⁴	I2D: score=1 STRING: ENSP00000292807
MME	P08473³	I2D: score=2

About this table

Gene Ontology (GO): 5/11 biological process terms (GO ID links to tree view) (see all 11): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006897	endocytosis	IEA	--
GO:0007159	leukocyte cell-cell adhesion	NAS	11337487
GO:0009988	cell-cell recognition	TAS	11337487
GO:0019048	virus-host interaction	TAS	11337487
GO:0019062	viral attachment to host cell	TAS	11337487

CLEC4M for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

CLEC4M for compounds About GeneDecksing

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for CLEC4M

1 HMDB Compound for CLEC4M About this table

Compound	Synonyms	CAS #	PubMed Ids
Calcium	Ca (see all 2)	7440-70-2	--

5 Novoseek chemical compound relationships for CLEC4M gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
mannose	58.7	4	11384997 (2), 16210905 (1), 17150970 (1)
polysaccharide	52.1	9	17621595 (2), 16210905 (1), 11384997 (1), 19249311 (1) (see all 5)
carbohydrates	26.6	2	18375037 (1)
galactose	23.9	2	16210905 (1), 14990712 (1)
allergens	18.2	2	16210905 (1), 20080962 (1)

Search CenterWatch for drugs/clinical trials and news about CLEC4M / CLC4M

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for CLEC4M gene (11 alternative transcripts):

NM_001144904.1 NM_001144905.1 NM_001144906.1 NM_001144907.1 NM_001144908.1 NM_001144909.1 NM_001144910.1 NM_001144911.1

NM_014257.4 NM_214675.1 NM_214676.1

Unigene Cluster for CLEC4M:

C-type lectin domain family 4, member M

Hs.421437 [show with all ESTs]

Unigene Representative Sequence: NR_026707

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000327325(uc002mih.3 uc010xjw.2 uc010dvt.3 uc010dvs.3 uc010xjx.2 uc002mia.3)

ENST00000394122(uc002mhy.2) ENST00000248228 ENST00000334806 ENST00000359059

ENST00000357361(uc010xjv.1 uc002mhz.3 uc002mic.3)

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Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CLEC4M (see all 7) OriGene shRNA RFP: CLEC4M OriGene siRNA: CLEC4M
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Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CLEC4M (see all 12) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CLEC4M (see all 9) OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 9): CLEC4M (NM_014257)
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		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLEC4M

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for CLEC4M Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat CLEC4M
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CLEC4M
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CLEC4M

Additional cDNA sequence:

AB015629.1 AF245219.2 AF290887.1 AK292278.1 AK298084.1 AK304499.1 AK314704.1 AY042234.1

AY042235.1 AY042236.1 AY042237.1 AY042238.1 AY042239.1 AY042240.1 AY343913.1 BC038851.1

BC110614.2 NR_026707.1 NR_026708.1 NR_026709.1

9 DOTS entries:

DT.113522 DT.100794824 DT.91734204 DT.95302819 DT.100794826 DT.95302830 DT.95302822 DT.113521

DT.91734201

24/54 AceView cDNA sequences (see all 54):

AL544658 AY042239 NM_014257 AF245219 AY042235 BE562903 NM_214678 AF290887

NM_214677 BQ006101 BI827055 AY343913 AY042236 BC038851 NM_214675 NM_214676

AV645629 AA431250 AY042234 AV645755 AA779963 CB162093 NM_214679 AB015629

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for CLEC4M About this scheme

ExUns:	1a	·	1b	^	2	^	3	^	4a	·	4b	·	4c	^	5	^	6	^	7a	·	7b	^	8
SP1:									-								-
SP2:							-										-
SP3:
SP4:							-		-
SP5:					-		-		-

ECgene alternative splicing isoforms for CLEC4M

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

CLEC4M expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TCTTCCATTT

About this image

CLEC4M expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

1 LifeMap In Vivo Development Anatomical Compartment/Cell

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Liver

Sinusoids

Sinusoidal Endothelial Cells

Endothelium

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See CLEC4M Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CLEC4M

SOURCE GeneReport for Unigene cluster: Hs.421437

UniProtKB/Swiss-Prot: CLC4M_HUMAN, Q9H2X3

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

SABiosciences Custom PCR Arrays for CLEC4M

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		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CLEC4M

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC4M

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for CLEC4M gene from 2/7 species (see all 7) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
lizard (Anolis carolinensis)	Reptilia	--	--	32(a)	1 → many	2(80104375-80116126)
zebrafish (Danio rerio)	Actinopterygii	zgc:174904⁶ si:ch211-170d8.5⁶ (see all 3)	si:ch211-170d8.5 (see all 3)	24(a) 19(a) (see all 3)	1 ↔ many possible ortholog (see all 3)	19(6313826-6322596) 8(41685924-41692286)

ENSEMBL Gene Tree for CLEC4M (if available)
TreeFam Gene Tree for CLEC4M (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for CLEC4M gene

CD207² CLEC4E² ASGR2² CLEC4F² CD209² CLEC10A² FCER2² CLEC4A²

CLEC6A² ASGR1² CLEC4C² CLEC4D² CLEC4G²

11 SIMAP similar genes for CLEC4M using alignment to 8 protein entries: CLC4M_HUMAN (see all proteins):

CD209 FCER2 CLEC4E CLEC6A CLEC4D CLEC4C

KLRD1 CLEC2B KLRG1 CLEC5A REG4

CLEC4M for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
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UniProtKB/Swiss-Prot: CLC4M_HUMAN, Q9H2X3

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

SNP ID	Valid	Clinical significance	Chr 19 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs12974826^1,2	C	--	7500843(+)	`CAGGAG/AATCTA`	1	--	int¹		1		NA	2
rs12974835^1,2	C,F,H	--	7500855(+)	`CAGGAG/ACTGAC`	1	--	int¹		9		NS EA	1286
rs12974848^1,2	C,H	--	7500871(+)	`TGAAGG/ACTGCA`	2	/T /A	mis¹ ese³		6		NS EA NA	500
rs148277440^1,2		--	7826068(+)	`CAGCTC/TCCTCT`	12	--	us2k¹		0	--	--	--	--
rs141408047^1,2		--	7826237(+)	`CCCCCC/TAACCT`	12	--	us2k¹		0	--	--	--	--
rs190419803^1,2		--	7826305(+)	`CAGATA/GTTTCC`	12	--	us2k¹		0	--	--	--	--
rs150832765^1,2		--	7826380(+)	`CCCACC/TGTTTA`	12	--	us2k¹		0	--	--	--	--
rs182199465^1,2		--	7826538(+)	`ATGGGC/TCAGGC`	12	--	us2k¹		0	--	--	--	--
rs139608770^1,2		--	7826604(+)	`CTTAAC/GGTCAG`	12	--	us2k¹		0	--	--	--	--
rs74915262^1,2	C,F,	--	7826637(+)	`ACATGG/ATGAAA`	12	--	us2k¹		7		NA WA CSA	13

HapMap Linkage Disequilibrium report for CLEC4M (7828035 - 7834491 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for CLEC4M
1 CNV: 8863
1 Indel: 26372
Human Gene Mutation Database (HGMD): CLEC4M

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

CLEC4M for disorders           About GeneDecksing

OMIM gene information: 605872    OMIM disorders: --

15 diseases for CLEC4M:    About MalaCards

sars infection, protection against sars infection severe acute respiratory syndrome hepatitis c

measles tuberculosis liver disease sinusitis

thrombosis hepatitis immunodeficiency influenza

leukemia venous thrombosis hiv type 1

1 disease from the University of Copenhagen DISEASES database for CLEC4M:

Severe acute respiratory syndrome

8 Novoseek disease relationships for CLEC4M gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
immunodeficiency	54.9	17	12502850 (2), 11226297 (2), 11799181 (1), 12477827 (1) (see all 13)
hepatitis c	42.8	13	19785948 (3), 12634366 (2), 16816373 (2), 15254204 (1) (see all 7)
virus infection	40.4	5	11739956 (1), 17502670 (1), 20003397 (1), 16051304 (1) (see all 5)
hiv infections	21.8	6	17530994 (2), 12152166 (2), 19046307 (1), 12738250 (1)
autoimmunity	17.1	2	16365436 (1)
infectious disease	16.1	3	16365436 (1), 20003397 (1)
tuberculosis	4.89	4	17321900 (3)
aids	0	3	12738250 (3)

Genetic Association Database (GAD): CLEC4M
Human Genome Epidemiology (HuGE) Navigator: CLEC4M (19 documents)

Export disorders for CLEC4M gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for CLEC4M gene, integrated from 9 sources (see all 123):
(articles sorted by number of sources associating them with CLEC4M)

Utopia: connect your pdf to the dynamic
world of online information

Selection of cDNAs encoding putative type II membrane proteins on the cell surface from a human full-length cDNA bank. (PubMed id 10072769)^{1, 2, 3} Yokoyama-Kobayashi M.... Kato S. (1999)
CD209L (L-SIGN) is a receptor for severe acute respiratory syndrome coronavirus. (PubMed id 15496474)^{1, 2, 9} Jeffers S.A.... Holmes K.V. (2004)
DC-SIGNR, a DC-SIGN homologue expressed in endothelial cells, binds to human and simian immunodeficiency viruses and activates infection in trans. (PubMed id 11226297)^{1, 2, 9} Poehlmann S.... Doms R.W. (2001)
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. (PubMed id 11337487)^{1, 2, 9} Mummidi S.... Ahuja S.K. (2001)
A novel mechanism of carbohydrate recognition by the C-type lectins DC-SIGN and DC-SIGNR. Subunit organization and binding to multivalent ligands. (PubMed id 11384997)^{1, 2, 9} Mitchell D.A.... Drickamer K. (2001)
Extended neck regions stabilize tetramers of the receptors DC-SIGN and DC-SIGNR. (PubMed id 15509576)^{1, 2, 9} Feinberg H.... Weis W.I. (2005)
L-SIGN (CD209L) and DC-SIGN (CD209) mediate transinfection of liver cells by hepatitis C virus. (PubMed id 15371595)^{1, 2, 9} Cormier E.G.... Dragic T. (2004)
Structural basis for selective recognition of oligosaccharides by DC- SIGN and DC-SIGNR. (PubMed id 11739956)^{1, 2, 9} Feinberg H.... Weis W.I. (2001)
Differential N-linked glycosylation of human immunodeficiency virus and Ebola virus envelope glycoproteins modulates interactions with DC- SIGN and DC-SIGNR. (PubMed id 12502850)^{1, 2, 9} Lin G.... Doms R.W. (2003)
DC-SIGN, a related gene, DC-SIGNR, and CD23 form a cluster on 19p13. (PubMed id 10975799)^{1, 2, 9} Soilleux E.J.... Trowsdale J. (2000)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 10332	HGNC: 13523	AceView: CD209L	Ensembl:ENSG00000104938	euGenes: HUgn10332
ECgene: CLEC4M	Kegg: 10332	H-InvDB: CLEC4M

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for CLEC4M	Pharmacogenomics, SNPs, Pathways
Functional Glycomics Gateway - Glycan Binding	http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_00122

Intellectual Property for CLEC4M gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for CLEC4M gene:
Search GeneIP for patents involving CLEC4M

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

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CLEC4M Gene

C-type lectin domain family 4, member M

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CLEC4M Gene

C-type lectin domain family 4, member M

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