LY6E

gene
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Also known as TSA-1RIG-ESCA-2

Summary

LY6E (lymphocyte antigen 6 family member E, HGNC:6727) is a protein-coding gene on chromosome 8q24.3, encoding Lymphocyte antigen 6E (Q16553). GPI-anchored cell surface protein that regulates T-lymphocytes proliferation, differentiation, and activation.

This gene belongs to the human Ly6 gene family and encodes a glycosylphosphatidyl-inositol (GPI)-anchored cell surface protein. The protein plays an important role in T cell physiology, oncogenesis and immunological regulation. The protein is also involved in modulation of viral infection by coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2.

Source: NCBI Gene 4061 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 38 total
  • Druggable target: yes
  • MANE Select transcript: NM_002346

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6727
Approved symbolLY6E
Namelymphocyte antigen 6 family member E
Location8q24.3
Locus typegene with protein product
StatusApproved
AliasesTSA-1, RIG-E, SCA-2
Ensembl geneENSG00000160932
Ensembl biotypeprotein_coding
OMIM601384
Entrez4061

Gene structure

Transcript identifiers

Ensembl transcripts: 50 — 49 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000292494, ENST00000429120, ENST00000517503, ENST00000519546, ENST00000519611, ENST00000519615, ENST00000520466, ENST00000520531, ENST00000521003, ENST00000521182, ENST00000521699, ENST00000522024, ENST00000522528, ENST00000522971, ENST00000523847, ENST00000891132, ENST00000891133, ENST00000891134, ENST00000891135, ENST00000891136, ENST00000891137, ENST00000891138, ENST00000891139, ENST00000891140, ENST00000891141, ENST00000891142, ENST00000891143, ENST00000891144, ENST00000891145, ENST00000891146, ENST00000891147, ENST00000891148, ENST00000891149, ENST00000891150, ENST00000891151, ENST00000891152, ENST00000891153, ENST00000891154, ENST00000891155, ENST00000891156, ENST00000891157, ENST00000891158, ENST00000891159, ENST00000891160, ENST00000891161, ENST00000891162, ENST00000891163, ENST00000964930, ENST00000964931, ENST00000964932

RefSeq mRNA: 2 — MANE Select: NM_002346 NM_001127213, NM_002346

CCDS: CCDS6394

Canonical transcript exons

ENST00000292494 — 4 exons

ExonStartEnd
ENSE00001141198143020883143020991
ENSE00002101953143018529143018586
ENSE00003469314143021314143021433
ENSE00003603930143021566143022409

Expression profiles

Bgee: expression breadth ubiquitous, 145 present calls, max score 99.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 181.7059 / max 2217.2817, expressed in 1817 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
91372146.48601808
9137132.16941798
913751.6558889
913741.2860718
913700.108736

Top tissues by expression

145 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111499.16gold quality
granulocyteCL:000009499.04gold quality
olfactory segment of nasal mucosaUBERON:000538698.95gold quality
liverUBERON:000210798.83gold quality
stromal cell of endometriumCL:000225598.81gold quality
placentaUBERON:000198798.78gold quality
right ovaryUBERON:000211898.70gold quality
right lungUBERON:000216798.66gold quality
upper lobe of left lungUBERON:000895298.66gold quality
Ammon’s hornUBERON:000195498.63gold quality
right frontal lobeUBERON:000281098.63gold quality
left adrenal glandUBERON:000123498.61gold quality
endocervixUBERON:000045898.60gold quality
left adrenal gland cortexUBERON:003582598.58gold quality
apex of heartUBERON:000209898.55gold quality
right adrenal gland cortexUBERON:003582798.52gold quality
nucleus accumbensUBERON:000188298.51gold quality
frontal cortexUBERON:000187098.50gold quality
putamenUBERON:000187498.50gold quality
ectocervixUBERON:001224998.50gold quality
right adrenal glandUBERON:000123398.49gold quality
right uterine tubeUBERON:000130298.46gold quality
prefrontal cortexUBERON:000045198.45gold quality
right hemisphere of cerebellumUBERON:001489098.44gold quality
spleenUBERON:000210698.42gold quality
dorsolateral prefrontal cortexUBERON:000983498.41gold quality
left uterine tubeUBERON:000130398.37gold quality
caudate nucleusUBERON:000187398.37gold quality
superior frontal gyrusUBERON:000266198.37gold quality
cerebellar hemisphereUBERON:000224598.34gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 11.

ExperimentMarker?Max mean expression
E-MTAB-10287yes108.44
E-HCAD-4yes58.47
E-GEOD-134144yes48.65
E-CURD-112yes22.63
E-HCAD-6yes20.51
E-ANND-3yes17.07
E-MTAB-9388yes14.40
E-MTAB-8142yes14.34
E-CURD-46yes13.62
E-HCAD-1yes12.17
E-MTAB-8498yes9.88
E-HCAD-13no1241.67
E-MTAB-10283no269.38

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HMGA1, HMGA2, POU2F1, POU2F2

miRNA regulators (miRDB)

27 targeting LY6E, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-449299.8768.253611
HSA-MIR-444799.8567.812900
HSA-MIR-120099.7170.421838
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-182799.6368.573265
HSA-MIR-9851-3P99.6369.681110
HSA-MIR-426999.5569.891373
HSA-MIR-486-3P99.5166.821901
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-593-5P99.3469.50965
HSA-MIR-450599.2767.812678
HSA-MIR-578799.2267.862628
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-1304-5P98.9068.581054
HSA-MIR-426098.7865.37848
HSA-MIR-4742-3P98.7369.821803
HSA-MIR-1227-5P98.6565.321549
HSA-MIR-63797.9164.051517
HSA-MIR-365297.7165.431890
HSA-MIR-443097.4765.611813

Literature-anchored findings (GeneRIF, showing 18)

  • Increased expression of the type I interferon-inducible gene, lymphocyte antigen 6 complex locus E, in peripheral blood cells is predictive of lupus activity in a large cohort of Chinese lupus patients. (PMID:18755862)
  • Two SCA3 and one SCA2 cases have been identified which show autosomal dominant inheritance in Parkinson disease. (PMID:18990604)
  • This study suggested that a mutation in SCA2 or SCA3/MJD may be one of the genetic causes of Parkinson’s disease in china. (PMID:19672991)
  • the LY6E pathway in monocytes represents one of negative feedback mechanisms that counterbalance monocyte activation which may serve as a potential target for immune intervention. (PMID:25225669)
  • LY6E level of gene expression may serve as good biomarkers for systemic lupus erythematosus diagnosis. (PMID:25344775)
  • LY6E overexpression is associated with Breast Cancer Progression, Immune Escape, and Drug Resistance. (PMID:27197181)
  • High LY6E expression is associated with breast cancer. (PMID:27589564)
  • LY6E is a positive modulator of HIV-1 infection in primary human peripheral blood mononuclear cells, immortalized CD4+ T lymphoid cells, and macrophages. HIV Long Terminal Repeat-driven HIV-1 gene expression is also enhanced by LY6E, suggesting additional roles of LY6E in HIV-1 replication. (PMID:28130445)
  • LY6E knockdown by targeted-siRNA inhibited gastric cancer cell survival and proliferation and induced G1-S cell cycle arrest and apoptosis in gastric cancer cells (PMID:29448250)
  • LY6E belongs to a growing class of interferon-inducible factors that broadly enhance viral infectivity in an interferon-independent manner. (PMID:30190477)
  • LY6E downregulates the cell surface receptor CD4. (PMID:30674630)
  • A Phase I Study of DLYE5953A, an Anti-LY6E Antibody Covalently Linked to Monomethyl Auristatin E, in Patients with Refractory Solid Tumors. (PMID:32694157)
  • Protein LY6E as a candidate for mediating transport of adeno-associated virus across the human blood-brain barrier. (PMID:32839948)
  • alpha5-nAChR associated with Ly6E modulates cell migration via TGF-beta1/Smad signaling in non-small cell lung cancer. (PMID:34994389)
  • Multidimension Analysis of the Prognostic Value, Immune Regulatory Function, and ceRNA Network of LY6E in Individuals with Colorectal Cancer. (PMID:35310607)
  • LY6E protein facilitates adeno-associated virus crossing in a biomimetic chip model of the human blood-brain barrier. (PMID:36165190)
  • Innovative biomarkers TCN2 and LY6E can significantly inhibit respiratory syncytial virus infection. (PMID:39313785)
  • Exploring Molecular Drivers of PARPi Resistance in BRCA1-Deficient Ovarian Cancer: The Role of LY6E and Immunomodulation. (PMID:39408764)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusLy6eENSMUSG00000022587
rattus_norvegicusLy6eENSRNOG00000007091

Paralogs (2): PSCA (ENSG00000167653), GPIHBP1 (ENSG00000277494)

Protein

Protein identifiers

Lymphocyte antigen 6EQ16553 (reviewed: Q16553)

Alternative names: Retinoic acid-induced gene E protein, Stem cell antigen 2, Thymic shared antigen 1

All UniProt accessions (6): Q16553, E5RGI6, E5RI33, E5RI58, E5RIQ1, E7EWF8

UniProt curated annotations — full annotation on UniProt →

Function. GPI-anchored cell surface protein that regulates T-lymphocytes proliferation, differentiation, and activation. Regulates the T-cell receptor (TCR) signaling by interacting with component CD3Z/CD247 at the plasma membrane, leading to CD3Z/CD247 phosphorylation modulation. Restricts the entry of human coronaviruses, including SARS-CoV, MERS-CoV and SARS-CoV-2, by interfering with spike protein-mediated membrane fusion. Also plays an essential role in placenta formation by acting as the main receptor for syncytin-A (SynA). Therefore, participates in the normal fusion of syncytiotrophoblast layer I (SynT-I) and in the proper morphogenesis of both fetal and maternal vasculatures within the placenta. May also act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. (Microbial infection) Promotes entry, likely through an enhanced virus-cell fusion process, of various viruses including HIV-1, West Nile virus, dengue virus and Zika virus. In contrast, the paramyxovirus PIV5, which enters at the plasma membrane, does not require LY6E. Mechanistically, adopts a microtubule-like organization upon viral infection and enhances viral uncoating after endosomal escape.

Subunit / interactions. Interacts with CHRNA4.

Subcellular location. Cell membrane.

Tissue specificity. Widely expressed, predominantly in liver, kidney, ovary, spleen and peripheral blood Leukocytes.

Induction. By retinoic acid; in promyelocytic leukemia NB4 and in myeloblast HL-60 cell lines. Activated by IFN-alpha in monocytic cell line U-937 and in peripheral blood monocyte cells.

RefSeq proteins (2): NP_001120685, NP_002337* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR016054LY6_UPA_recep-likeDomain
IPR035076Toxin/TOLIPDomain
IPR045860Snake_toxin-like_sfHomologous_superfamily
IPR051110Ly-6/neurotoxin-like_GPI-apFamily

Pfam: PF00087

UniProt features (14 total): disulfide bond 5, mutagenesis site 3, signal peptide 1, chain 1, propeptide 1, domain 1, lipid moiety-binding region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q16553-F177.970.32

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): 101

Disulfide bonds (5): 93–98, 23–48, 26–35, 41–71, 75–92

Glycosylation sites (1): 99

Mutagenesis-validated functional residues (3):

PositionPhenotype
36complete loss of viral entry enhancement. abolishes inhibition of human coronaviruses entry.
57about 50% loss of viral entry enhancement.
99abolishes inhibition of human coronaviruses entry.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-163125Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-9918485Dengue Virus Attachment and Entry
R-HSA-392499Metabolism of proteins
R-HSA-597592Post-translational protein modification

MSigDB gene sets: 342 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, YAGI_AML_WITH_INV_16_TRANSLOCATION, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, ENK_UV_RESPONSE_KERATINOCYTE_UP, MODULE_64, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, GOBP_MODULATION_OF_PROCESS_OF_ANOTHER_ORGANISM, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP

GO Biological Process (3): cell surface receptor signaling pathway (GO:0007166), host-mediated suppression of symbiont invasion (GO:0046597), acetylcholine receptor signaling pathway (GO:0095500)

GO Molecular Function (3): acetylcholine receptor inhibitor activity (GO:0030550), acetylcholine receptor binding (GO:0033130), protein binding (GO:0005515)

GO Cellular Component (5): extracellular region (GO:0005576), plasma membrane (GO:0005886), synapse (GO:0045202), side of membrane (GO:0098552), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Post-translational protein modification1
Dengue Virus Infection1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
acetylcholine receptor activity2
membrane2
signal transduction1
innate immune response1
host-mediated perturbation of symbiont process1
postsynaptic signal transduction1
cellular response to acetylcholine1
signaling receptor inhibitor activity1
acetylcholine receptor regulator activity1
signaling receptor binding1
binding1
cell periphery1
cell junction1
leaflet of membrane bilayer1

Protein interactions and networks

STRING

820 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LY6EPSCAO43653896
LY6EIFI44LQ53G44710
LY6EIFI6P09912686
LY6EOAS1P00973673
LY6ERSPH1Q8WYR4656
LY6EMX1P20591607
LY6EEPSTI1Q96J88592
LY6EIFI44Q8TCB0582
LY6EISG15P05161580
LY6EIFIT3O14879574
LY6ECD59P13987561
LY6ERSAD2Q8WXG1541
LY6EIFITM3Q01628530
LY6EIFIT1P09914524
LY6EERVW-1Q9UQF0522

IntAct

17 interactions, top by confidence:

ABTypeScore
TUSC5LY6Epsi-mi:“MI:0915”(physical association)0.560
TMEM19LY6Epsi-mi:“MI:0915”(physical association)0.560
LY6ETMEM19psi-mi:“MI:0915”(physical association)0.560
LY6EMFSD6psi-mi:“MI:0915”(physical association)0.560
LY6ETMEM140psi-mi:“MI:0915”(physical association)0.560
repLY6Epsi-mi:“MI:0915”(physical association)0.560
SLC22A1FNDC10psi-mi:“MI:0914”(association)0.350
MFSD6LY6Epsi-mi:“MI:0915”(physical association)0.000
TMEM140LY6Epsi-mi:“MI:0915”(physical association)0.000

BioGRID (22): CD247 (Affinity Capture-Western), LY6E (Affinity Capture-RNA), LY6E (Two-hybrid), LY6E (Two-hybrid), LY6E (Two-hybrid), TUSC5 (Two-hybrid), LY6E (Affinity Capture-RNA), LY6E (Two-hybrid), PHB (Affinity Capture-MS), HSP90AA1 (Affinity Capture-MS), HSP90AB1 (Affinity Capture-MS), EEF1G (Affinity Capture-MS), EIF4A1 (Affinity Capture-MS), PHB (Affinity Capture-Western), HSP90AA1 (Affinity Capture-Western)

ESM2 similar proteins: B3MFC2, B3NSF6, B4QBL6, B5A5T4, B5E022, D3ZTT2, D4A6L0, H3BQJ8, O43653, P12645, P19438, P22444, P23352, P46657, P49002, P50555, P57096, P58658, P58659, Q16553, Q1RMB5, Q28216, Q32LD3, Q505J3, Q568T5, Q5R510, Q5T848, Q66IA6, Q68US5, Q6UWL2, Q6UWN0, Q6UX15, Q6WN34, Q80XH4, Q86Y78, Q8BHE5, Q8BPP5, Q8BVP6, Q8C351, Q8C419

Diamond homologs: A0JNB3, O94772, P0DTL4, Q16553, Q4R5M8, Q63317, Q90986, Q9WU67, Q9WUC3, O43653, P0DP58, P57096, Q6UXB3, H3BJG9, P05533, P0CW02, P0CW03, P35460, P35461, Q64253, A0A346CIB2, Q9DD23, P55000, Q9Z0K7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

38 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance19
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

998 predictions. Top by Δscore:

VariantEffectΔscore
8:143020989:GAGGT:Gdonor_loss1.0000
8:143020991:GG:Gdonor_loss1.0000
8:143020992:G:GCdonor_loss1.0000
8:143021309:C:Aacceptor_gain1.0000
8:143021312:A:AGacceptor_gain1.0000
8:143021313:G:GAacceptor_gain1.0000
8:143021313:GCC:Gacceptor_gain1.0000
8:143021313:GCCA:Gacceptor_gain1.0000
8:143021431:TTG:Tdonor_gain1.0000
8:143021431:TTGGT:Tdonor_loss1.0000
8:143021432:TG:Tdonor_gain1.0000
8:143021432:TGG:Tdonor_loss1.0000
8:143021433:GG:Gdonor_gain1.0000
8:143021434:G:GAdonor_loss1.0000
8:143021434:G:GGdonor_gain1.0000
8:143021435:TGAG:Tdonor_loss1.0000
8:143018696:G:GTdonor_gain0.9900
8:143018974:G:Tdonor_gain0.9900
8:143020881:A:AGacceptor_gain0.9900
8:143020882:G:GGacceptor_gain0.9900
8:143020882:G:Tacceptor_gain0.9900
8:143020882:GA:Gacceptor_gain0.9900
8:143020882:GAGCA:Gacceptor_gain0.9900
8:143020987:GCGAG:Gdonor_gain0.9900
8:143021308:CCGCA:Cacceptor_loss0.9900
8:143021309:CGCAG:Cacceptor_loss0.9900
8:143021310:GCAG:Gacceptor_loss0.9900
8:143021311:CAGC:Cacceptor_loss0.9900
8:143021312:AG:Aacceptor_loss0.9900
8:143021313:GC:Gacceptor_gain0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000146671 (8:143016732 T>A,C), RS1001490623 (8:143017043 G>A), RS1002229761 (8:143018122 C>T), RS1002353141 (8:143020526 A>T), RS1002899792 (8:143017956 C>A,G), RS1003257317 (8:143020803 C>T), RS1003624371 (8:143019405 G>T), RS1003638150 (8:143019716 A>T), RS1004060446 (8:143019659 G>A,C), RS1004845844 (8:143022257 G>A), RS1005066347 (8:143016623 T>C), RS1005153751 (8:143020491 C>A), RS1005169132 (8:143016675 A>C), RS1005444732 (8:143017033 G>C), RS1006070634 (8:143017826 G>A)

Disease associations

OMIM: gene MIM:601384 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4523584 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

60 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tretinoindecreases reaction, affects cotreatment, increases expression, increases reaction6
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression5
Cyclosporineincreases expression, decreases expression3
Arsenic Trioxidedecreases reaction, increases expression, affects cotreatment2
Estradiolaffects cotreatment, decreases expression, increases expression2
Plant Extractsdecreases expression, affects cotreatment2
Tobacco Smoke Pollutiondecreases expression, increases expression2
bisphenol Aincreases expression1
cobaltous chloridedecreases expression1
2-bromopalmitateincreases expression, increases reaction1
perfluorooctanoic acidincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
potassium chromate(VI)increases expression1
hydroquinonedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
tamibaroteneincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
erucylphospho-N,N,N-trimethylpropylammoniumdecreases expression1
ICG 001decreases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
jinfukangaffects cotreatment, increases expression1
NSC 689534affects binding, decreases expression1
(+)-JQ1 compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1

Cellosaurus cell lines

2 cell lines: 1 spontaneously immortalized cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E6R4Genomeditech CHO-K1 H_LY6ESpontaneously immortalized cell lineFemale
CVCL_E6UHGenomeditech HEK-293 H_LY6ETransformed cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.