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Aliases for SLAMF6 Gene

Aliases for SLAMF6 Gene

  • SLAM Family Member 6 2 3 5
  • Activating NK Receptor 3 4
  • NK-T-B-Antigen 3 4
  • NTB-A 3 4
  • KALI 3 4
  • Natural Killer-, T- And B-Cell Antigen 3
  • NTBA Receptor 3
  • CD352 Antigen 4
  • SF2000 3
  • CD352 3
  • KALIb 3
  • Ly108 3
  • NTBA 3

External Ids for SLAMF6 Gene

Previous GeneCards Identifiers for SLAMF6 Gene

  • GC01M157671
  • GC01M157267
  • GC01M158721
  • GC01M131811

Summaries for SLAMF6 Gene

Entrez Gene Summary for SLAMF6 Gene

  • The protein encoded by this gene is a type I transmembrane protein, belonging to the CD2 subfamily of the immunoglobulin superfamily. This encoded protein is expressed on Natural killer (NK), T, and B lymphocytes. It undergoes tyrosine phosphorylation and associates with the Src homology 2 domain-containing protein (SH2D1A) as well as with SH2 domain-containing phosphatases (SHPs). It functions as a coreceptor in the process of NK cell activation. It can also mediate inhibitory signals in NK cells from X-linked lymphoproliferative patients. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010]

GeneCards Summary for SLAMF6 Gene

SLAMF6 (SLAM Family Member 6) is a Protein Coding gene. Diseases associated with SLAMF6 include Systemic Lupus Erythematosus and Bare Lymphocyte Syndrome, Type I. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. Gene Ontology (GO) annotations related to this gene include receptor activity. An important paralog of this gene is CD84.

UniProtKB/Swiss-Prot for SLAMF6 Gene

  • Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. Triggers cytolytic activity only in natural killer cells (NK) expressing high surface densities of natural cytotoxicity receptors (PubMed:11489943, PubMed:16920955). Positive signaling in NK cells implicates phosphorylation of VAV1. NK cell activation seems to depend on SH2D1B and not on SH2D1A (PubMed:16920955). In conjunction with SLAMF1 controls the transition between positive selection and the subsequent expansion and differentiation of the thymocytic natural killer T (NKT) cell lineage (By similarity). Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727, PubMed:16920955). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). In conjunction with SLAMF1 and CD84/SLAMF5 may be a negative regulator of the humoral immune response. In the absence of SH2D1A/SAP can transmit negative signals to CD4(+) T-cells and NKT cells. Negatively regulates germinal center formation by inhibiting T-cell:B-cell adhesion; the function probably implicates increased association with PTPN6/SHP-1 via ITSMs in absence of SH2D1A/SAP. However, reported to be involved in maintaining B-cell tolerance in germinal centers and in preventing autoimmunity (By similarity).

Gene Wiki entry for SLAMF6 Gene

Additional gene information for SLAMF6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLAMF6 Gene

Genomics for SLAMF6 Gene

GeneHancer (GH) Regulatory Elements for SLAMF6 Gene

Promoters and enhancers for SLAMF6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I160518 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 553.8 +2.0 1967 4.7 HDGF PKNOX1 SMAD1 IRF4 ZNF766 E2F8 ZNF143 ATF7 RUNX3 JUNB SLAMF6 VANGL2 CD84 SLAMF1 LOC105371467
GH01I160573 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.6 -53.7 -53675 6.1 PKNOX1 RB1 ARNT BMI1 ZBTB40 ZNF766 EGR1 ATF7 FOS BCLAF1 CD84 SLAMF7 VANGL2 SLAMF6 SLAMF1 CD48 CD244 ATP1A4 LOC105371468
GH01I161096 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.3 -574.4 -574416 2.9 YBX1 FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 MCM3 KLHDC9 USP21 DUSP12 PPOX LOC100287049 DEDD NCSTN RPSAP18 LOC148430 DCAF8
GH01I160436 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 14.6 +85.2 85201 2.5 PKNOX1 IRF2 TEAD4 TAL1 BACH1 CEBPG RBBP5 BATF GATA3 GATA2 LOC105371467 SLAMF6 USP21 SLAMF1 PPOX CD84 VANGL2 ENSG00000228863 ITLN1 LY9
GH01I160565 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 12.5 -44.6 -44646 5 HDGF BATF IRF4 ZBTB40 ZNF766 EGR1 ATF7 ETV6 RUNX3 CBFB CD84 VANGL2 SLAMF6 ATP1A4 SLAMF1 LY9 CD48 LOC105371468
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLAMF6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLAMF6 gene promoter:

Genomic Locations for SLAMF6 Gene

Genomic Locations for SLAMF6 Gene
chr1:160,485,030-160,523,262
(GRCh38/hg38)
Size:
38,233 bases
Orientation:
Minus strand
chr1:160,454,820-160,493,052
(GRCh37/hg19)

Genomic View for SLAMF6 Gene

Genes around SLAMF6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLAMF6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLAMF6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLAMF6 Gene

Proteins for SLAMF6 Gene

  • Protein details for SLAMF6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DU3-SLAF6_HUMAN
    Recommended name:
    SLAM family member 6
    Protein Accession:
    Q96DU3
    Secondary Accessions:
    • A6NMW2
    • B2R8X8
    • Q14CF0
    • Q5TAS4
    • Q5TAS6
    • Q5TAT3
    • Q96DV0

    Protein attributes for SLAMF6 Gene

    Size:
    332 amino acids
    Molecular mass:
    37345 Da
    Quaternary structure:
    • Homodimer. Interacts with PTN6. Interacts (phosphorylated) with PTN11. Interacts (phosphorylated on tyrosine residues) with SH2D1A/SAP and SH2D1B/EAT2; SH2D1A and SH2D1B can associate with the same SLAMF6 molecule; interaction with SH2D1B is mediated by ITSM 2.

    Three dimensional structures from OCA and Proteopedia for SLAMF6 Gene

    Alternative splice isoforms for SLAMF6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLAMF6 Gene

Post-translational modifications for SLAMF6 Gene

  • Phosphorylation in NK cells upon engagment by SLAMF6-expressing target cells is leading to receptor activation.
  • Glycosylation at posLast=5858, posLast=8787, posLast=137137, isoforms=2, 3144, posLast=161161, posLast=171171, isoforms=2, 3178, and isoforms=2, 3203

No data available for DME Specific Peptides for SLAMF6 Gene

Domains & Families for SLAMF6 Gene

Protein Domains for SLAMF6 Gene

Graphical View of Domain Structure for InterPro Entry

Q96DU3

UniProtKB/Swiss-Prot:

SLAF6_HUMAN :
  • The ITSMs (immunoreceptor tyrosine-based switch motifs) with the consensus sequence T-X-Y-X-X-[VI] present in SLAM family receptors have overlapping specificity for activating and inhibitory SH2 domain-containingbinding partners. Especially they mediate the with the SH2 domain of SH2D1A and SH2D1B. A two-out-of-three-pronged mechanism is proposed involving threonine (position -2), phosphorylated tyrosine (position 0) and valine/isoleucine (position +3).
Domain:
  • The ITSMs (immunoreceptor tyrosine-based switch motifs) with the consensus sequence T-X-Y-X-X-[VI] present in SLAM family receptors have overlapping specificity for activating and inhibitory SH2 domain-containingbinding partners. Especially they mediate the with the SH2 domain of SH2D1A and SH2D1B. A two-out-of-three-pronged mechanism is proposed involving threonine (position -2), phosphorylated tyrosine (position 0) and valine/isoleucine (position +3).
genes like me logo Genes that share domains with SLAMF6: view

Function for SLAMF6 Gene

Molecular function for SLAMF6 Gene

UniProtKB/Swiss-Prot Function:
Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. Triggers cytolytic activity only in natural killer cells (NK) expressing high surface densities of natural cytotoxicity receptors (PubMed:11489943, PubMed:16920955). Positive signaling in NK cells implicates phosphorylation of VAV1. NK cell activation seems to depend on SH2D1B and not on SH2D1A (PubMed:16920955). In conjunction with SLAMF1 controls the transition between positive selection and the subsequent expansion and differentiation of the thymocytic natural killer T (NKT) cell lineage (By similarity). Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727, PubMed:16920955). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). In conjunction with SLAMF1 and CD84/SLAMF5 may be a negative regulator of the humoral immune response. In the absence of SH2D1A/SAP can transmit negative signals to CD4(+) T-cells and NKT cells. Negatively regulates germinal center formation by inhibiting T-cell:B-cell adhesion; the function probably implicates increased association with PTPN6/SHP-1 via ITSMs in absence of SH2D1A/SAP. However, reported to be involved in maintaining B-cell tolerance in germinal centers and in preventing autoimmunity (By similarity).

Phenotypes From GWAS Catalog for SLAMF6 Gene

Gene Ontology (GO) - Molecular Function for SLAMF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11489943
genes like me logo Genes that share ontologies with SLAMF6: view
genes like me logo Genes that share phenotypes with SLAMF6: view

Animal Models for SLAMF6 Gene

MGI Knock Outs for SLAMF6:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for SLAMF6 Gene

Localization for SLAMF6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLAMF6 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLAMF6 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SLAMF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome IDA,HDA 20458337
genes like me logo Genes that share ontologies with SLAMF6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLAMF6 Gene

Pathways & Interactions for SLAMF6 Gene

genes like me logo Genes that share pathways with SLAMF6: view

Pathways by source for SLAMF6 Gene

Gene Ontology (GO) - Biological Process for SLAMF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002376 immune system process IEA --
GO:0032729 positive regulation of interferon-gamma production IMP 16920955
GO:0032740 positive regulation of interleukin-17 production IDA 22184727
GO:0045087 innate immune response IEA --
GO:0045954 positive regulation of natural killer cell mediated cytotoxicity IDA 16920955
genes like me logo Genes that share ontologies with SLAMF6: view

No data available for SIGNOR curated interactions for SLAMF6 Gene

Drugs & Compounds for SLAMF6 Gene

(1) Drugs for SLAMF6 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SLAMF6: view

Transcripts for SLAMF6 Gene

Unigene Clusters for SLAMF6 Gene

SLAM family member 6:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLAMF6 Gene

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

Relevant External Links for SLAMF6 Gene

GeneLoc Exon Structure for
SLAMF6
ECgene alternative splicing isoforms for
SLAMF6

Expression for SLAMF6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLAMF6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLAMF6 Gene

This gene is overexpressed in Whole Blood (x13.3) and Spleen (x8.0).

Protein differential expression in normal tissues from HIPED for SLAMF6 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (35.3), CD8 Tcells (13.3), and Lymph node (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLAMF6 Gene



Protein tissue co-expression partners for SLAMF6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SLAMF6 Gene:

SLAMF6

SOURCE GeneReport for Unigene cluster for SLAMF6 Gene:

Hs.492348

mRNA Expression by UniProt/SwissProt for SLAMF6 Gene:

Q96DU3-SLAF6_HUMAN
Tissue specificity: Expressed by all (resting and activated) natural killer cells (NK), T- and B-lymphocytes (PubMed:11489943). Increased surface expression on T-cells of systemic lupus erythematosus (SLE) patients (PubMed:22184727).

Evidence on tissue expression from TISSUES for SLAMF6 Gene

  • Lymph node(4.5)
  • Spleen(4.4)
  • Blood(2.3)
genes like me logo Genes that share expression patterns with SLAMF6: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLAMF6 Gene

Orthologs for SLAMF6 Gene

This gene was present in the common ancestor of mammals.

Orthologs for SLAMF6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLAMF6 33 34
  • 98.69 (n)
cow
(Bos Taurus)
Mammalia SLAMF6 33 34
  • 71.63 (n)
dog
(Canis familiaris)
Mammalia SLAMF6 33 34
  • 66.98 (n)
rat
(Rattus norvegicus)
Mammalia Slamf6 33
  • 65.21 (n)
mouse
(Mus musculus)
Mammalia Slamf6 33 16 34
  • 64.6 (n)
oppossum
(Monodelphis domestica)
Mammalia SLAMF6 34
  • 27 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 22 (a)
ManyToMany
Species where no ortholog for SLAMF6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for SLAMF6 Gene

ENSEMBL:
Gene Tree for SLAMF6 (if available)
TreeFam:
Gene Tree for SLAMF6 (if available)

Paralogs for SLAMF6 Gene

Paralogs for SLAMF6 Gene

Pseudogenes.org Pseudogenes for SLAMF6 Gene

genes like me logo Genes that share paralogs with SLAMF6: view

Variants for SLAMF6 Gene

Sequence variations from dbSNP and Humsavar for SLAMF6 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000023641 -- 160,507,285(-) A/G intron_variant
rs1000061811 -- 160,488,105(-) A/C/G intron_variant
rs1000125259 -- 160,506,776(-) A/G intron_variant
rs1000238990 -- 160,520,557(-) T/C intron_variant
rs1000288483 -- 160,490,738(-) G/C intron_variant

Variation tolerance for SLAMF6 Gene

Residual Variation Intolerance Score: 17% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.46; 10.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLAMF6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLAMF6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SLAMF6 Gene

Disorders for SLAMF6 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SLAMF6 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SLAMF6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLAMF6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLAMF6 Gene

Publications for SLAMF6 Gene

  1. NTB-A [correction of GNTB-A], a novel SH2D1A-associated surface molecule contributing to the inability of natural killer cells to kill Epstein-Barr virus-infected B cells in X-linked lymphoproliferative disease. (PMID: 11489943) Bottino C … Moretta A (The Journal of experimental medicine 2001) 2 3 4 22 58
  2. NTB-A receptor crystal structure: insights into homophilic interactions in the signaling lymphocytic activation molecule receptor family. (PMID: 17045824) Cao E … Almo SC (Immunity 2006) 3 4 22 58
  3. CD3-T cell receptor co-stimulation through SLAMF3 and SLAMF6 receptors enhances RORγt recruitment to the IL17A promoter in human T lymphocytes. (PMID: 22989874) Chatterjee M … Tsokos GC (The Journal of biological chemistry 2012) 3 4 58
  4. Increased expression of SLAM receptors SLAMF3 and SLAMF6 in systemic lupus erythematosus T lymphocytes promotes Th17 differentiation. (PMID: 22184727) Chatterjee M … Tsokos GC (Journal of immunology (Baltimore, Md. : 1950) 2012) 3 4 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for SLAMF6 Gene

Sources for SLAMF6 Gene

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