LY9
gene geneOn this page
Also known as CD229mLY9SLAMF3hly9
Summary
LY9 (lymphocyte antigen 9, HGNC:6730) is a protein-coding gene on chromosome 1q23.3, encoding T-lymphocyte surface antigen Ly-9 (Q9HBG7). Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family.
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]).
Source: NCBI Gene 4063 — RefSeq curated summary.
At a glance
- GWAS associations: 5
- Clinical variants (ClinVar): 115 total
- MANE Select transcript:
NM_002348
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:6730 |
| Approved symbol | LY9 |
| Name | lymphocyte antigen 9 |
| Location | 1q23.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | CD229, mLY9, SLAMF3, hly9 |
| Ensembl gene | ENSG00000122224 |
| Ensembl biotype | protein_coding |
| OMIM | 600684 |
| Entrez | 4063 |
Gene structure
Transcript identifiers
Ensembl transcripts: 17 — 11 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron
ENST00000263285, ENST00000368035, ENST00000368037, ENST00000368039, ENST00000392203, ENST00000471816, ENST00000474998, ENST00000479663, ENST00000480837, ENST00000485624, ENST00000490902, ENST00000873847, ENST00000873848, ENST00000873849, ENST00000873850, ENST00000873851, ENST00000873852
RefSeq mRNA: 4 — MANE Select: NM_002348
NM_001033667, NM_001261456, NM_001261457, NM_002348
CCDS: CCDS30916, CCDS30917, CCDS65695, CCDS65696
Canonical transcript exons
ENST00000263285 — 10 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000789190 | 160819321 | 160819374 |
| ENSE00000789192 | 160824181 | 160824249 |
| ENSE00000958829 | 160796174 | 160796311 |
| ENSE00000958831 | 160823465 | 160823796 |
| ENSE00001166088 | 160816594 | 160816863 |
| ENSE00001228897 | 160818218 | 160818319 |
| ENSE00001228917 | 160827748 | 160828255 |
| ENSE00003500890 | 160799753 | 160800082 |
| ENSE00003540463 | 160813636 | 160813911 |
| ENSE00003634771 | 160814420 | 160814761 |
Expression profiles
Bgee: expression breadth ubiquitous, 181 present calls, max score 92.00.
FANTOM5 (CAGE): breadth broad, TPM avg 7.7981 / max 648.1966, expressed in 347 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 6182 | 6.1085 | 326 |
| 6183 | 1.0305 | 181 |
| 6180 | 0.4329 | 121 |
| 6181 | 0.1295 | 68 |
| 6179 | 0.0966 | 59 |
Top tissues by expression
283 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| granulocyte | CL:0000094 | 92.00 | gold quality |
| lymph node | UBERON:0000029 | 91.21 | gold quality |
| buccal mucosa cell | CL:0002336 | 90.86 | gold quality |
| blood | UBERON:0000178 | 89.44 | gold quality |
| spleen | UBERON:0002106 | 88.10 | gold quality |
| bone marrow cell | CL:0002092 | 87.05 | gold quality |
| colonic epithelium | UBERON:0000397 | 85.61 | gold quality |
| bone marrow | UBERON:0002371 | 84.74 | gold quality |
| superficial temporal artery | UBERON:0001614 | 83.42 | gold quality |
| vermiform appendix | UBERON:0001154 | 82.99 | gold quality |
| trabecular bone tissue | UBERON:0002483 | 82.29 | gold quality |
| tonsil | UBERON:0002372 | 82.26 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 82.08 | gold quality |
| nasopharynx | UBERON:0001728 | 82.07 | gold quality |
| amniotic fluid | UBERON:0000173 | 80.25 | gold quality |
| caecum | UBERON:0001153 | 79.99 | gold quality |
| thymus | UBERON:0002370 | 79.08 | gold quality |
| olfactory bulb | UBERON:0002264 | 77.77 | gold quality |
| type B pancreatic cell | CL:0000169 | 77.71 | gold quality |
| parotid gland | UBERON:0001831 | 76.34 | gold quality |
| rectum | UBERON:0001052 | 76.10 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 75.14 | gold quality |
| leukocyte | CL:0000738 | 74.73 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 74.35 | gold quality |
| small intestine | UBERON:0002108 | 73.53 | gold quality |
| gall bladder | UBERON:0002110 | 73.38 | gold quality |
| mononuclear cell | CL:0000842 | 73.00 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 72.97 | gold quality |
| monocyte | CL:0000576 | 72.93 | gold quality |
| jejunal mucosa | UBERON:0000399 | 72.06 | gold quality |
Single-cell (SCXA)
Detected in 8 experiment(s), a significant marker in 7.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-135922 | yes | 878.75 |
| E-CURD-122 | yes | 93.67 |
| E-CURD-88 | yes | 51.49 |
| E-ANND-3 | yes | 36.43 |
| E-MTAB-8142 | yes | 14.73 |
| E-MTAB-6678 | yes | 4.60 |
| E-MTAB-9067 | yes | 4.53 |
| E-ENAD-27 | no | 3.93 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
21 targeting LY9, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-1252-5P | 100.00 | 69.80 | 2774 |
| HSA-MIR-4673 | 100.00 | 66.64 | 1490 |
| HSA-MIR-6499-3P | 99.90 | 66.38 | 1212 |
| HSA-MIR-12119 | 99.87 | 68.35 | 1653 |
| HSA-MIR-4649-3P | 99.56 | 66.90 | 1783 |
| HSA-MIR-4506 | 99.34 | 67.47 | 526 |
| HSA-MIR-12113 | 99.32 | 67.54 | 1072 |
| HSA-MIR-4291 | 99.20 | 68.88 | 2969 |
| HSA-MIR-4504 | 99.10 | 69.14 | 1328 |
| HSA-MIR-4650-3P | 99.01 | 68.39 | 1062 |
| HSA-MIR-6770-5P | 98.97 | 66.76 | 1853 |
| HSA-MIR-3074-5P | 98.82 | 66.56 | 1414 |
| HSA-MIR-4539 | 98.78 | 67.18 | 888 |
| HSA-MIR-581 | 98.39 | 67.42 | 835 |
| HSA-MIR-599 | 98.32 | 66.99 | 1037 |
| HSA-MIR-595 | 98.25 | 67.44 | 699 |
| HSA-MIR-3921 | 97.81 | 67.45 | 1431 |
| HSA-MIR-6747-3P | 97.73 | 64.84 | 1596 |
| HSA-MIR-4653-5P | 97.22 | 67.72 | 1429 |
| HSA-MIR-592 | 96.59 | 67.59 | 817 |
| HSA-MIR-3675-5P | 95.90 | 65.80 | 474 |
Literature-anchored findings (GeneRIF, showing 22)
- Both mouse and human novel Ly9 genes mapped close to the CD229 gene in a region where other members of the CD150 family have also been mapped. (PMID:12242590)
- CD229, but not other members of the CD150 family, directly bind Grb2. (PMID:15879090)
- CD229 is a self-ligand, interacting through its N-terminal V-like domain which contains three amino acid residues critical for the homophilic binding interaction. (PMID:15905546)
- A family-based association study in the United Kingdom and Canada identifies genetic variants in the LY9 promoter and coding region contributing to systemic lupus erythematosus susceptibility. (PMID:18216865)
- CD229 is specifically over-expressed on myeloma cells including their clonogenic precursors and contributes to their malignant phenotype. (PMID:21606160)
- SLAMF3 and SLAMF6 T cell surface expression and IL-17 levels significantly correlate with disease activity in systemic lupus erythematosus patients (PMID:22184727)
- Data indicate that the dominance of the SLAMF3/SLAMF6 pathway in inducing IL-17A production can be attributed to an increased nuclear abundance and recruitment of RORgammat to the IL17A promoter. (PMID:22989874)
- These results suggest a role for CD319 and CD229 in the systemic lupus erythematosus disease process. (PMID:23956418)
- SLAMF3 is an inhibitor of hepatocellular carcinoma cell proliferation and tumor progression. (PMID:24376606)
- Results revealed that SLAMF3 plays a role during hepatitis C virus entry, likely by enhancing entry of viral particle within hepatocytes. (PMID:24927415)
- study showed CD229 is overexpressed on the malignant plasma cells of patients across all types of plasma cell dyscrasias including multiple myeloma; CD229 is also expressed on the surface of a fraction of cells carrying the phenotype of chemotherapy-resistant and myeloma-propagating cells within the patients’ bone marrow (PMID:26001047)
- the Val602 variant of the non-synonymous single nucleotide polymorphism (SNP) rs509749 in the SLAM family member CD229 (Ly9, SLAMF3) has a two-fold lower affinity compared with the SLE-associated Met602 variant for the small adaptor protein SAP (PMID:26221972)
- CD229 Expression on Bone Marrow Plasma Cells from Patients with Multiple Myeloma and Monoclonal Gammopathies of Uncertain Significance. (PMID:26303094)
- the results presented here suggest that the tumor suppressor potential of SLAMF3 occurs through activation of Retinoblastoma protein that represses PLK1. (PMID:26799423)
- Authors make a strong correlation between induced SLAMF3 overexpression and the specific loss of MRP-1 expression and its functionalities as a drugs resistance transporter. (PMID:27081035)
- CD229 is a reliable new alternative PC-gating marker in routine laboratory practice. (PMID:29316178)
- Viral Ly9 homologs are new manipulators of host immunity. (Review) (PMID:30791129)
- SLAMF3 expression is upregulated on T cells from type 2 diabetes patients and associated with T-cell activation and cytokine production. (PMID:31332162)
- SLAMF3-Mediated Signaling via ERK Pathway Activation Promotes Aggressive Phenotypic Behaviors in Multiple Myeloma. (PMID:31974290)
- The SLAMF3 rs509749 polymorphism correlates with malignant potential in multiple myeloma. (PMID:32818503)
- CD229 interacts with RASAL3 to activate RAS/ERK pathway in multiple myeloma proliferation. (PMID:36445333)
- SLAMF3 promotes Th17 differentiation and is reversed by iguratimod through JAK1/STAT3 pathway in primary Sjogren’s syndrome. (PMID:38061117)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | si:cabz01074946.1 | ENSDARG00000090396 |
| mus_musculus | Ly9 | ENSMUSG00000004707 |
| rattus_norvegicus | Ly9 | ENSRNOG00000025069 |
Paralogs (9): SLAMF7 (ENSG00000026751), CD84 (ENSG00000066294), CD2 (ENSG00000116824), SLAMF1 (ENSG00000117090), CD48 (ENSG00000117091), CD244 (ENSG00000122223), SLAMF8 (ENSG00000158714), SLAMF9 (ENSG00000162723), SLAMF6 (ENSG00000162739)
Protein
Protein identifiers
T-lymphocyte surface antigen Ly-9 — Q9HBG7 (reviewed: Q9HBG7)
Alternative names: Cell surface molecule Ly-9, Lymphocyte antigen 9, SLAM family member 3, Signaling lymphocytic activation molecule 3
All UniProt accessions (6): A0A0C4DFU4, Q5VYH9, Q5VYI1, Q9HBG7, R4GNG7, V9GY30
UniProt curated annotations — full annotation on UniProt →
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. Promotes recruitment of RORC to the IL-17 promoter. 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.
Subunit / interactions. Interacts with SH2D1A, SH2D1B and INPP5D. Interacts (via phosphorylated cytoplasmic domain) with PTPN11; the interaction is blocked by SH2D1A.
Subcellular location. Membrane. Cell membrane.
Tissue specificity. Increased surface expression on T-cells of systemic lupus erythematosus (SLE) patients.
Domain organisation. 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).
Isoforms (4)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9HBG7-1 | 1 | yes |
| Q9HBG7-2 | 2 | |
| Q9HBG7-3 | 3 | |
| Q9HBG7-4 | 4 |
RefSeq proteins (4): NP_001028839, NP_001248385, NP_001248386, NP_002339* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR003599 | Ig_sub | Domain |
| IPR007110 | Ig-like_dom | Domain |
| IPR013783 | Ig-like_fold | Homologous_superfamily |
| IPR015631 | CD2/SLAM_rcpt | Family |
| IPR036179 | Ig-like_dom_sf | Homologous_superfamily |
UniProt features (33 total): glycosylation site 8, disulfide bond 4, splice variant 4, domain 4, region of interest 2, short sequence motif 2, topological domain 2, signal peptide 1, chain 1, compositionally biased region 1, modified residue 1, transmembrane region 1, sequence variant 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9HBG7-F1 | 66.27 | 0.24 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (1): 603
Disulfide bonds (4): 172–242, 178–222, 377–446, 383–427
Glycosylation sites (8): 68, 95, 120, 169, 173, 285, 413, 424
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 253 (showing top):
GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, MORF_MSH3, MODULE_255, GOBP_T_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, MORF_BRCA1, GOBP_ALPHA_BETA_T_CELL_DIFFERENTIATION, MODULE_317, GOCC_CELL_SURFACE, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_CD4_POSITIVE_ALPHA_BETA_T_CELL_ACTIVATION, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_T_CELL_DIFFERENTIATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_CYTOKINE_PRODUCTION, GOBP_POSITIVE_T_CELL_SELECTION
GO Biological Process (8): immune response (GO:0006955), cell adhesion (GO:0007155), positive regulation of interleukin-17 production (GO:0032740), T cell activation (GO:0042110), innate immune response (GO:0045087), T-helper 17 cell lineage commitment (GO:0072540), adaptive immune response (GO:0002250), immune system process (GO:0002376)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (4): plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), cell surface (GO:0009986), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| immune response | 2 |
| cellular anatomical structure | 2 |
| immune system process | 1 |
| response to stimulus | 1 |
| cellular process | 1 |
| positive regulation of cytokine production | 1 |
| interleukin-17 production | 1 |
| regulation of interleukin-17 production | 1 |
| lymphocyte activation | 1 |
| defense response to symbiont | 1 |
| T-helper cell lineage commitment | 1 |
| T-helper 17 cell differentiation | 1 |
| biological_process | 1 |
| binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| plasma membrane | 1 |
| cell surface | 1 |
| side of membrane | 1 |
Protein interactions and networks
STRING
1324 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| LY9 | SH2D1B | O14796 | 937 |
| LY9 | SH2D1A | O60880 | 932 |
| LY9 | CD48 | P09326 | 925 |
| LY9 | CD2 | P06729 | 750 |
| LY9 | SLAMF1 | Q13291 | 637 |
| LY9 | SLAMF8 | Q9P0V8 | 627 |
| LY9 | CD58 | P19256 | 589 |
| LY9 | PTPN11 | Q06124 | 575 |
| LY9 | NCR1 | O76036 | 511 |
| LY9 | SRC | P12931 | 495 |
| LY9 | DOK2 | O60496 | 479 |
| LY9 | GRB2 | P29354 | 464 |
| LY9 | CD244 | Q9BZW8 | 461 |
| LY9 | VAV1 | P15498 | 459 |
| LY9 | ATP1A2 | P50993 | 458 |
IntAct
6 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SH2D1A | LY9 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| INPP5D | LY9 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| LY9 | LY9 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| LY9 | GUSB | psi-mi:“MI:0914”(association) | 0.350 |
| LY9 | purL | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (12): AP2M1 (Two-hybrid), LY9 (Affinity Capture-Western), LY9 (Two-hybrid), LY9 (Affinity Capture-Western), LY9 (Two-hybrid), PTPN11 (Affinity Capture-Western), Sh2d1b1 (Affinity Capture-Western), EDEM3 (Affinity Capture-MS), GUSB (Affinity Capture-MS), HLA-F (Affinity Capture-MS), DDX19B (Affinity Capture-MS), IDUA (Affinity Capture-MS)
ESM2 similar proteins: A0A0B4J1G0, A0A0B4J1L0, A0A0G2KBC9, A1YIY0, A8MTB9, B6A8R8, C0HJX2, C0HJX3, E2RP87, H0VDZ8, P08637, P09326, P12314, P23505, P26151, P43626, P43627, P43628, P43631, P43632, P83555, P83556, Q01965, Q13291, Q14952, Q14953, Q14954, Q28942, Q2YHT5, Q61400, Q61450, Q640U3, Q68EV1, Q68SN8, Q6UX41, Q6UXE8, Q6UY09, Q6XJV4, Q6XPU4, Q7TST0
Diamond homologs: A4FUY1, A6QQC6, A8MVW5, D3YXG0, D3ZB51, D3ZQE1, E9PZ19, O08775, P13595, P13596, P16573, P31809, P35968, P52583, Q00889, Q14CZ8, Q3KPI0, Q4VAH7, Q52KR2, Q62845, Q640R3, Q69Z26, Q9D2Z1, Q9HBG7, Q9UPX0, Q01965, Q18PI6, Q8BHK6, Q96A28, Q96DU3, Q9D780, Q9NQ25, Q9UIB8, O94898, P35918, Q5GIT4, Q810J1, Q9ET39, P11464, Q00887
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
115 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 92 |
| Likely benign | 11 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1760 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:160796310:GG:G | donor_gain | 1.0000 |
| 1:160796311:GG:G | donor_gain | 1.0000 |
| 1:160816725:G:GT | donor_gain | 1.0000 |
| 1:160796307:CATGG:C | donor_gain | 0.9900 |
| 1:160796309:TGG:T | donor_gain | 0.9900 |
| 1:160796309:TGGG:T | donor_loss | 0.9900 |
| 1:160796310:GGG:G | donor_gain | 0.9900 |
| 1:160796310:GGGTA:G | donor_loss | 0.9900 |
| 1:160796311:GGTAA:G | donor_loss | 0.9900 |
| 1:160796312:G:GG | donor_gain | 0.9900 |
| 1:160796312:GT:G | donor_loss | 0.9900 |
| 1:160796313:TAAG:T | donor_loss | 0.9900 |
| 1:160799899:C:G | acceptor_gain | 0.9900 |
| 1:160814762:G:GG | donor_gain | 0.9900 |
| 1:160818318:GT:G | donor_gain | 0.9900 |
| 1:160818320:G:GG | donor_gain | 0.9900 |
| 1:160796308:ATGG:A | donor_gain | 0.9800 |
| 1:160800079:TATGG:T | donor_loss | 0.9800 |
| 1:160800080:ATGG:A | donor_loss | 0.9800 |
| 1:160800081:TGG:T | donor_loss | 0.9800 |
| 1:160800082:GGTGA:G | donor_loss | 0.9800 |
| 1:160800083:GTG:G | donor_loss | 0.9800 |
| 1:160800084:T:A | donor_loss | 0.9800 |
| 1:160800085:G:GT | donor_loss | 0.9800 |
| 1:160818314:G:GT | donor_gain | 0.9800 |
| 1:160827746:AGGT:A | acceptor_gain | 0.9800 |
| 1:160827747:GGTG:G | acceptor_gain | 0.9800 |
| 1:160800086:AGT:A | donor_loss | 0.9700 |
| 1:160800087:G:C | donor_loss | 0.9700 |
| 1:160816826:G:GT | donor_gain | 0.9700 |
AlphaMissense
4280 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:160813754:G:C | W191C | 0.989 |
| 1:160813754:G:T | W191C | 0.989 |
| 1:160799868:G:C | W80C | 0.987 |
| 1:160799868:G:T | W80C | 0.987 |
| 1:160799866:T:A | W80R | 0.986 |
| 1:160799866:T:C | W80R | 0.986 |
| 1:160813845:T:A | C222S | 0.986 |
| 1:160813846:G:C | C222S | 0.986 |
| 1:160800064:T:C | F146L | 0.985 |
| 1:160800066:C:A | F146L | 0.985 |
| 1:160800066:C:G | F146L | 0.985 |
| 1:160813752:T:A | W191R | 0.985 |
| 1:160813752:T:C | W191R | 0.985 |
| 1:160813845:T:C | C222R | 0.984 |
| 1:160813847:C:G | C222W | 0.984 |
| 1:160800013:T:G | Y129D | 0.982 |
| 1:160813713:T:C | C178R | 0.981 |
| 1:160813846:G:A | C222Y | 0.981 |
| 1:160813713:T:A | C178S | 0.979 |
| 1:160813714:G:C | C178S | 0.979 |
| 1:160814535:G:C | W282C | 0.978 |
| 1:160814535:G:T | W282C | 0.978 |
| 1:160814692:T:G | Y335D | 0.977 |
| 1:160813708:T:C | L176P | 0.974 |
| 1:160814533:T:A | W282R | 0.974 |
| 1:160814533:T:C | W282R | 0.974 |
| 1:160816800:T:A | C427S | 0.974 |
| 1:160816801:G:C | C427S | 0.974 |
| 1:160800020:C:A | A131D | 0.973 |
| 1:160816709:G:C | W396C | 0.972 |
dbSNP variants (sampled 300 via entrez): RS1000015217 (1:160828446 T>A), RS1000058821 (1:160801974 G>A,T), RS1000111302 (1:160804457 T>G), RS1000162886 (1:160808757 T>C,G), RS1000258158 (1:160822485 C>T), RS1000376027 (1:160797156 A>G), RS1000462995 (1:160810668 C>T), RS1000505412 (1:160806254 C>T), RS1000569578 (1:160807663 G>A), RS1000754138 (1:160794729 A>G), RS1001134693 (1:160819110 C>CAG), RS1001289060 (1:160816184 C>A,T), RS1001327563 (1:160797798 T>C), RS1001362819 (1:160804189 C>T), RS1001532608 (1:160821159 A>C)
Disease associations
OMIM: gene MIM:600684 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
5 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST004627_130 | Lymphocyte count | 3.000000e-11 |
| GCST004632_97 | Lymphocyte percentage of white cells | 2.000000e-11 |
| GCST90002388_629 | Lymphocyte count | 5.000000e-39 |
| GCST90002389_75 | Lymphocyte percentage of white cells | 4.000000e-18 |
| GCST90002407_8 | White blood cell count | 6.000000e-09 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004587 | lymphocyte count |
| EFO:0007993 | lymphocyte percentage of leukocytes |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
23 total (human), top 23 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | increases expression | 2 |
| Nickel | increases expression | 2 |
| triphenyl phosphate | affects expression | 1 |
| perfluorooctanoic acid | increases expression | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects response to substance, increases expression, affects cotreatment, decreases expression | 1 |
| avobenzone | increases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| K 7174 | decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| theaflavin-3,3’-digallate | affects expression | 1 |
| Arsenic | affects methylation | 1 |
| Aspirin | increases expression | 1 |
| Benzo(a)pyrene | affects methylation | 1 |
| Cadmium | increases expression | 1 |
| Hydrogen Peroxide | decreases expression | 1 |
| Ibuprofen | decreases expression | 1 |
| Lipopolysaccharides | increases expression, affects cotreatment, decreases expression, affects response to substance | 1 |
| Testosterone | decreases expression | 1 |
| Tobacco Smoke Pollution | increases expression | 1 |
| Urethane | decreases expression | 1 |
| Antirheumatic Agents | decreases expression | 1 |
| Cadmium Chloride | increases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.