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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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LY9
lymphocyte antigen 9
Chromosome 1 · 1q23.3
NCBI Gene: 4063Ensembl: ENSG00000122224.19HGNC: HGNC:6730UniProt: A0A0C4DFU4
41PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
T-helper 17 cell lineage commitmentpositive regulation of interleukin-17 productionplasma membraneimmune responseCINCA syndromehepatocellular carcinomaMiyoshi myopathylung adenocarcinoma
✦AI Summary

LY9 (lymphocyte antigen 9, also known as CD229 or SLAMF3) is a self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family expressed predominantly on B and T cells 1. As a homophilic adhesion molecule, LY9 regulates lymphocyte activation and differentiation through homo- or heterotypic cell-cell interactions, with activity controlled by adapter proteins SH2D1A/SAP and SH2D1B/EAT-2 2. LY9 promotes T-cell differentiation toward a Th17 phenotype by recruiting RORC to the IL-17 promoter and enhances Th1* cell polarization through SAP-dependent and SAP-independent mechanisms involving T-bet and RORγT 2. Mechanistically, LY9 costimulation enhances TCR-driven IFN-γ production in memory Th1* cells via NFAT1 and RORγT signaling 2. Clinically, autosomal recessive LY9 deficiency causes tuberculosis susceptibility due to selective impairment of Th1*-mediated IFN-γ production 2. LY9 has emerged as a potential therapeutic target in multiple diseases: it is associated with disease progression and disability severity in multiple sclerosis as part of an 11-protein CSF biomarker panel 3, implicated in diabetic retinopathy pathogenesis through immune-inflammatory pathways 4, and identified as a therapeutic candidate in lymphoma with downregulated expression in diffuse large B-cell lymphoma cells 5. Additionally, LY9 variants show rare enrichment in focal segmental glomerulosclerosis 6.

Sources cited
1
LY9 is a SLAM family receptor governing CD4+ T-cell differentiation into Th1* cells and IFN-γ production; autosomal recessive deficiency causes TB susceptibility; mechanistic pathway involves SAP, T-bet, RORγT, NFAT1
PMID: 40446017
2
LY9 is part of an 11-protein CSF biomarker panel predicting MS disability progression with AUC=0.90
PMID: 37903821
3
LY9 identified as core therapeutic target in diabetic retinopathy through immune-inflammatory pathways; influences DR subtypes via metabolic and inflammatory risk factors
PMID: 41340073
4
LY9 is a potential therapeutic target for lymphoma; downregulated in DLBCL cells; enriched in B-cell expression
PMID: 41222800
5
CD229/LY9 is a SLAMF homophilic receptor on B and T cells regulating lymphocyte homeostasis and activation; target of viral immune evasion
PMID: 30791129
6
LY9 identified as highly-ranked new gene with rare variant enrichment in focal segmental glomerulosclerosis cases
PMID: 31308072
7
LY9 is a genetic PML risk gene enriched in specific CD4+ and CD8+ T-cell populations in cerebrospinal fluid during progressive multifocal leukoencephalopathy
PMID: 38917802
8
LY9 highly expressed in FCRL1+ B-cell subset enriched in chronic hepatitis B immune-activation phase patients
PMID: 40489024
Disease Associationsⓘ20
CINCA syndromeOpen Targets
0.18Weak
hepatocellular carcinomaOpen Targets
0.10Weak
Miyoshi myopathyOpen Targets
0.10Suggestive
lung adenocarcinomaOpen Targets
0.08Suggestive
colorectal carcinomaOpen Targets
0.07Suggestive
neoplasmOpen Targets
0.07Suggestive
systemic lupus erythematosusOpen Targets
0.07Suggestive
chronic lymphocytic leukemiaOpen Targets
0.06Suggestive
type 2 diabetes mellitusOpen Targets
0.06Suggestive
multiple myelomaOpen Targets
0.06Suggestive
hepatitis C virus infectionOpen Targets
0.05Suggestive
severe combined immunodeficiency due to CARD11 deficiencyOpen Targets
0.04Suggestive
SepsisOpen Targets
0.04Suggestive
combined immunodeficiency due to CTPS1 deficiencyOpen Targets
0.04Suggestive
immunodeficiency 18Open Targets
0.04Suggestive
Duane retraction syndromeOpen Targets
0.04Suggestive
reticular dysgenesisOpen Targets
0.04Suggestive
lymphomaOpen Targets
0.04Suggestive
Wiskott-Aldrich syndromeOpen Targets
0.03Suggestive
diffuse large B-cell lymphomaOpen Targets
0.03Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
SH2D1AProtein interaction98%CD48Protein interaction95%SH2D1BProtein interaction94%CD2Protein interaction81%SLAMF6Protein interaction73%SLAMF1Protein interaction71%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
82%
Liver
28%
Brain
9%
Ovary
9%
Heart
6%
Gene Interaction Network
Click a node to explore
LY9SH2D1ACD48SH2D1BCD2SLAMF6SLAMF1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q05CA2
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.10LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.88 [0.71–1.10]
RankingsWhere LY9 stands among ~20K protein-coding genes
  • #10,031of 20,598
    Most Researched41
  • #11,196of 17,882
    Most Constrained (LOEUF)1.10
Genes detectedLY9
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Contributions of Rare Gene Variants to Familial and Sporadic FSGS.
PMID: 31308072
J Am Soc Nephrol · 2019
1.00
2
Human LY9 governs CD4
PMID: 40446017
Sci Immunol · 2025
0.90
3
Proteomics reveal biomarkers for diagnosis, disease activity and long-term disability outcomes in multiple sclerosis.
PMID: 37903821
Nat Commun · 2023
0.80
4
Multi-omics integrated analysis identifies causal risk factors and therapeutic targets for diabetic retinopathy.
PMID: 41340073
J Transl Med · 2025
0.70
5
Proteome-wide mendelian randomization identifies FCRL3 and LY9 as potential therapeutic targets for lymphoma.
PMID: 41222800
Discov Oncol · 2025
0.60