LY9 belongs to the SLAM family of immunomodulatory receptors (see SLAMF1; MIM 603492) and interacts with the adaptor molecule SAP (SH2D1A; MIM 300490) (Graham et al., 2006 [PubMed 16365421]).[supplied by OMIM, Mar 2008] See more...

Aliases for LY9 Gene

Aliases for LY9 Gene

  • Lymphocyte Antigen 9 2 3 4 5
  • SLAMF3 2 3 4
  • Signaling Lymphocytic Activation Molecule 3 3 4
  • T-Lymphocyte Surface Antigen Ly-9 3 4
  • Cell Surface Molecule Ly-9 3 4
  • SLAM Family Member 3 3 4
  • CD229 2 3
  • Hly9 2 3
  • MLY9 2 3
  • CD229 Antigen 4
  • LY9 5

External Ids for LY9 Gene

Previous GeneCards Identifiers for LY9 Gene

  • GC01P158558
  • GC01P156498
  • GC01P157543
  • GC01P157982
  • GC01P157579
  • GC01P159032
  • GC01P160765
  • GC01P132122

Summaries for LY9 Gene

Entrez Gene Summary for LY9 Gene

  • LY9 belongs to the SLAM family of immunomodulatory receptors (see SLAMF1; MIM 603492) and interacts with the adaptor molecule SAP (SH2D1A; MIM 300490) (Graham et al., 2006 [PubMed 16365421]).[supplied by OMIM, Mar 2008]

GeneCards Summary for LY9 Gene

LY9 (Lymphocyte Antigen 9) is a Protein Coding gene. Diseases associated with LY9 include Lymphoproliferative Syndrome and Selective Immunoglobulin Deficiency Disease. Among its related pathways are Hematopoietic Stem Cells and Lineage-specific Markers. An important paralog of this gene is CD84.

UniProtKB/Swiss-Prot Summary for LY9 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. May participate in adhesion reactions between T lymphocytes and accessory cells by homophilic interaction. Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). May be involved in the maintenance of peripheral cell tolerance by serving as a negative regulator of the immune response. May disable autoantibody responses and inhibit IFN-gamma secretion by CD4(+) T-cells. May negatively regulate the size of thymic innate CD8(+) T-cells and the development of invariant natural killer T (iNKT) cells (By similarity).

Gene Wiki entry for LY9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LY9 Gene

Genomics for LY9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LY9 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LY9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LY9

Top Transcription factor binding sites by QIAGEN in the LY9 gene promoter:
  • AML1a
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alpha isoform 3
  • AP-2alpha isoform 4
  • AP-2alphaA

Genomic Locations for LY9 Gene

Genomic Locations for LY9 Gene
chr1:160,796,074-160,828,261
(GRCh38/hg38)
Size:
32,188 bases
Orientation:
Plus strand
chr1:160,765,864-160,798,051
(GRCh37/hg19)
Size:
32,188 bases
Orientation:
Plus strand

Genomic View for LY9 Gene

Genes around LY9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LY9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LY9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LY9 Gene

Proteins for LY9 Gene

  • Protein details for LY9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBG7-LY9_HUMAN
    Recommended name:
    T-lymphocyte surface antigen Ly-9
    Protein Accession:
    Q9HBG7
    Secondary Accessions:
    • A8K7N3
    • Q14775
    • Q5VYI3
    • Q6P2J4
    • Q9H4N5
    • Q9NQ24

    Protein attributes for LY9 Gene

    Size:
    655 amino acids
    Molecular mass:
    72139 Da
    Quaternary structure:
    • Interacts with SH2D1A, SH2D1B and INPP5D. Interacts (via phosphorylated cytoplasmic domain) with PTPN11; the interaction is blocked by SH2D1A.

    Alternative splice isoforms for LY9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LY9 Gene

Post-translational modifications for LY9 Gene

  • Glycosylation at Asn68, Asn95, Asn120, Asn169, Asn173, Asn285, Asn413, and Asn424
  • Modification sites at PhosphoSitePlus

Assay Products

No data available for DME Specific Peptides for LY9 Gene

Domains & Families for LY9 Gene

Gene Families for LY9 Gene

HGNC:
Human Protein Atlas (HPA):
  • CD markers
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for LY9 Gene

InterPro:
Blocks:
  • Immunoglobulin subtype
ProtoNet:

Suggested Antigen Peptide Sequences for LY9 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ56843, highly similar to T-lymphocyte surface antigen Ly-9 (B4E0J5_HUMAN)
  • Lymphocyte antigen 9 (LY9_HUMAN)
  • LY9 protein (Q05CA2_HUMAN)
  • LY9 protein (Q0VAI0_HUMAN)
  • Lymphocyte antigen 9 (Q9UIB4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9HBG7

UniProtKB/Swiss-Prot:

LY9_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-containing binding partners. Especially they mediate the interaction with the SH2 domain of SH2D1A and SH2D1B. A '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-containing binding partners. Especially they mediate the interaction with the SH2 domain of SH2D1A and SH2D1B. A '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 LY9: view

Function for LY9 Gene

Molecular function for LY9 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. May participate in adhesion reactions between T lymphocytes and accessory cells by homophilic interaction. Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). May be involved in the maintenance of peripheral cell tolerance by serving as a negative regulator of the immune response. May disable autoantibody responses and inhibit IFN-gamma secretion by CD4(+) T-cells. May negatively regulate the size of thymic innate CD8(+) T-cells and the development of invariant natural killer T (iNKT) cells (By similarity).
GENATLAS Biochemistry:
lymphocyte surface antigen,murine Ly-9,immunoglobulin superfamily,putatively involved in adhesion reaction between T lymphocyte and accessory cells

Phenotypes From GWAS Catalog for LY9 Gene

Gene Ontology (GO) - Molecular Function for LY9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with LY9: view
genes like me logo Genes that share phenotypes with LY9: view

Animal Models for LY9 Gene

MGI Knock Outs for LY9:
  • Ly9 Ly9<tm1Mckn>

Animal Model Products

  • Taconic Biosciences Mouse Models for LY9

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LY9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for LY9 Gene

Localization for LY9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LY9 Gene

Membrane. Single-pass type I membrane protein. Cell membrane.

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 LY9 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LY9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA,IDA 22184727
GO:0009986 cell surface IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LY9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LY9 Gene

Pathways & Interactions for LY9 Gene

genes like me logo Genes that share pathways with LY9: view

Pathways by source for LY9 Gene

1 R&D Systems pathway for LY9 Gene

Gene Ontology (GO) - Biological Process for LY9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0007155 cell adhesion IEA --
GO:0032740 positive regulation of interleukin-17 production IDA 22184727
GO:0045087 innate immune response IEA --
genes like me logo Genes that share ontologies with LY9: view

No data available for SIGNOR curated interactions for LY9 Gene

Drugs & Compounds for LY9 Gene

(1) Drugs for LY9 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with LY9: view

Transcripts for LY9 Gene

mRNA/cDNA for LY9 Gene

4 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LY9

Alternative Splicing Database (ASD) splice patterns (SP) for LY9 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b · 14c ^ 15a ·
SP1: - - - - - -
SP2: - - - - - - -
SP3: - -
SP4: -
SP5: -
SP6: - -
SP7: - - - -
SP8: - -
SP9: - - - - -
SP10: - - -
SP11: - - - - -

ExUns: 15b ^ 16
SP1:
SP2:
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for LY9 Gene

GeneLoc Exon Structure for
LY9

Expression for LY9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LY9 Gene

mRNA differential expression in normal tissues according to GTEx for LY9 Gene

This gene is overexpressed in Whole Blood (x17.1) and Spleen (x8.6).

Protein differential expression in normal tissues from HIPED for LY9 Gene

This gene is overexpressed in CD4 Tcells (27.6), Peripheral blood mononuclear cells (23.6), and CD8 Tcells (13.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LY9 Gene



Protein tissue co-expression partners for LY9 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LY9

SOURCE GeneReport for Unigene cluster for LY9 Gene:

Hs.403857

mRNA Expression by UniProt/SwissProt for LY9 Gene:

Q9HBG7-LY9_HUMAN
Tissue specificity: Increased surface expression on T-cells of systemic lupus erythematosus (SLE) patients.

Evidence on tissue expression from TISSUES for LY9 Gene

  • Blood(4.6)
  • Spleen(4.6)
  • Lymph node(2.7)
  • Bone marrow(2.6)
  • Kidney(2)
genes like me logo Genes that share expression patterns with LY9: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for LY9 Gene

Orthologs for LY9 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LY9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LY9 30 31
  • 98.52 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LY9 30 31
  • 76.45 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LY9 30 31
  • 76.3 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ly9 30 17 31
  • 71.22 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ly9 30
  • 70.98 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia LY9 31
  • 33 (a)
OneToOne
Species where no ortholog for LY9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Oppossum (Monodelphis domestica)
  • 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 Vase (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 LY9 Gene

ENSEMBL:
Gene Tree for LY9 (if available)
TreeFam:
Gene Tree for LY9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LY9: view image

Paralogs for LY9 Gene

Paralogs for LY9 Gene

(3) SIMAP similar genes for LY9 Gene using alignment to 12 proteins:

  • LY9_HUMAN
  • E7EME5_HUMAN
  • F6W597_HUMAN
  • Q05CA2_HUMAN
  • Q0VAI0_HUMAN
  • Q5VYH8_HUMAN
  • Q5VYH9_HUMAN
  • Q5VYI1_HUMAN
  • Q9UIB4_HUMAN
  • Q9UIB5_HUMAN
  • R4GNG7_HUMAN
  • V9GY30_HUMAN
genes like me logo Genes that share paralogs with LY9: view

Variants for LY9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LY9 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
726709 Likely Benign: not provided 160,818,307(+) C/T NONSENSE
729550 Likely Benign: not provided 160,796,226(+) T/C SYNONYMOUS_VARIANT
783299 Benign: not provided 160,813,767(+) C/A MISSENSE_VARIANT
rs509749 - p.Met602Val

Additional dbSNP identifiers (rs#s) for LY9 Gene

Structural Variations from Database of Genomic Variants (DGV) for LY9 Gene

Variant ID Type Subtype PubMed ID
dgv84n67 CNV loss 20364138
esv2662152 CNV deletion 23128226
esv2671152 CNV deletion 23128226
esv3578224 CNV loss 25503493
esv3587718 CNV loss 21293372
nsv548057 CNV loss 21841781
nsv825087 CNV loss 20364138
nsv831714 CNV gain 17160897

Variation tolerance for LY9 Gene

Residual Variation Intolerance Score: 89.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.55; 44.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LY9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LY9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LY9 Gene

Disorders for LY9 Gene

MalaCards: The human disease database

(7) MalaCards diseases for LY9 Gene - From: DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LY9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LY9

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LY9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LY9 Gene

Publications for LY9 Gene

  1. Isolation and characterization of cDNA clones for Humly9: the human homologue of mouse Ly9. (PMID: 8537117) Sandrin MS … McKenzie IF (Immunogenetics 1996) 2 3 4
  2. A polymorphism in a phosphotyrosine signalling motif of CD229 (Ly9, SLAMF3) alters SH2 domain binding and T-cell activation. (PMID: 26221972) Margraf S … Brown MH (Immunology 2015) 3 4
  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
  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
  5. Association of LY9 in UK and Canadian SLE families. (PMID: 18216865) Cunninghame Graham DS … CaNIOS GenES Investigators (Genes and immunity 2008) 3 41

Products for LY9 Gene

Sources for LY9 Gene