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Aliases for LTA Gene

Aliases for LTA Gene

  • Lymphotoxin Alpha 2 3 5
  • Tumor Necrosis Factor Ligand Superfamily Member 1 3 4
  • LT-Alpha 3 4
  • TNF-Beta 3 4
  • TNFSF1 3 4
  • TNFB 3 4
  • Lymphotoxin Alpha (TNF Superfamily, Member 1) 2
  • Tumor Necrosis Factor Ligand 1E 3
  • Truncated Lymphotoxin Alpha 3
  • Tumor Necrosis Factor Beta 3
  • TNF Superfamily, Member 1 3
  • TNF Superfamily Member 1 2
  • Lymphotoxin-Alpha 3
  • TNLG1E 3
  • LT 3

External Ids for LTA Gene

Previous HGNC Symbols for LTA Gene

  • TNFB

Previous GeneCards Identifiers for LTA Gene

  • GC06P031603
  • GC06P031593
  • GC06P031310
  • GC06P031644
  • GC06P031648
  • GC06P031540
  • GC06P031541
  • GC06P031326
  • GC06P031572

Summaries for LTA Gene

Entrez Gene Summary for LTA Gene

  • The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

GeneCards Summary for LTA Gene

LTA (Lymphotoxin Alpha) is a Protein Coding gene. Diseases associated with LTA include Psoriatic Arthritis and Leprosy 4. Among its related pathways are PEDF Induced Signaling and Cytokine Signaling in Immune system. Gene Ontology (GO) annotations related to this gene include receptor binding and tumor necrosis factor receptor binding. An important paralog of this gene is TNF.

UniProtKB/Swiss-Prot for LTA Gene

  • Cytokine that in its homotrimeric form binds to TNFRSF1A/TNFR1, TNFRSF1B/TNFBR and TNFRSF14/HVEM. In its heterotrimeric form with LTB binds to TNFRSF3/LTBR. Lymphotoxin is produced by lymphocytes and cytotoxic for a wide range of tumor cells in vitro and in vivo.

Gene Wiki entry for LTA Gene

Additional gene information for LTA Gene

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

Genomics for LTA Gene

GeneHancer (GH) Regulatory Elements for LTA Gene

Promoters and enhancers for LTA 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
GH06I031567 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 550.4 +17.9 17869 22.2 HDGF PKNOX1 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 YBX1 ZNF2 TNF LST1 GC06P031585 GC06P031586 GC06P031587 GC06P031598 GC06P031599 GC06P031612 GC06P031613 GC06P031616
GH06I031557 Enhancer 1.2 Ensembl ENCODE 550.8 -1.0 -959 4.2 HDGF ATF1 SMAD1 IRF4 NCOA2 TCF12 E2F8 ZNF207 ZNF143 ATF7 LTA CSNK2B DDX39B LST1 NCR3 UQCRHP1 LTB AIF1 SNORD117 PSORS1C2
GH06I031562 Enhancer 0.8 FANTOM5 550.8 +1.7 1690 0.4 EBF1 BATF ZFHX2 ATF7 ETV6 IKZF2 RUNX3 EGR2 NR2F1 TRIM22 LTA TNF ATP6V1G2 STK19 HLA-B LST1 HSPA1B LOC100287329
GH06I031563 Enhancer 1.4 FANTOM5 Ensembl ENCODE 0.8 +2.9 2927 1.6 HDGF ATF1 ARNT NCOA2 TCF12 GATA2 E2F8 FOS NCOA1 MEF2D TNF MICB BAG6 CCHCR1 CSNK2B DHX16 ATP6V1G2 HLA-C HCG23 HLA-B
GH06I031551 Enhancer 0.7 ENCODE 0.4 -9.0 -9001 0.2 CTCF FOXA2 RAD21 CC2D1A CTBP1 FOXK2 ARID2 ZNF143 SMC3 ZNF600 MICB HLA-C LY6G5C NFKBIL1 ATP6V1G2 LTA LOC100287329
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LTA on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for LTA Gene

Genomic Locations for LTA Gene
chr6:31,560,550-31,574,324
(GRCh38/hg38)
Size:
13,775 bases
Orientation:
Plus strand
chr6:31,539,831-31,542,101
(GRCh37/hg19)

Genomic View for LTA Gene

Genes around LTA on UCSC Golden Path with GeneCards custom track

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

Proteins for LTA Gene

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

    Protein Symbol:
    P01374-TNFB_HUMAN
    Recommended name:
    Lymphotoxin-alpha
    Protein Accession:
    P01374
    Secondary Accessions:
    • Q8N4C3
    • Q9UKS8

    Protein attributes for LTA Gene

    Size:
    205 amino acids
    Molecular mass:
    22297 Da
    Quaternary structure:
    • Homotrimer, and heterotrimer of either two LTB and one LTA subunits or (less prevalent) two LTA and one LTB subunits.

    Three dimensional structures from OCA and Proteopedia for LTA Gene

neXtProt entry for LTA Gene

Post-translational modifications for LTA Gene

  • Glycosylation at posLast=4141 and isoforms=96

Other Protein References for LTA Gene

No data available for DME Specific Peptides for LTA Gene

Domains & Families for LTA Gene

Gene Families for LTA Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry

P01374

UniProtKB/Swiss-Prot:

TNFB_HUMAN :
  • Belongs to the tumor necrosis factor family.
Family:
  • Belongs to the tumor necrosis factor family.
genes like me logo Genes that share domains with LTA: view

Function for LTA Gene

Molecular function for LTA Gene

GENATLAS Biochemistry:
lymphotoxin alpha,expressed in T cells,tumors necrosis factor (ligand) superfamily,member 1
UniProtKB/Swiss-Prot Function:
Cytokine that in its homotrimeric form binds to TNFRSF1A/TNFR1, TNFRSF1B/TNFBR and TNFRSF14/HVEM. In its heterotrimeric form with LTB binds to TNFRSF3/LTBR. Lymphotoxin is produced by lymphocytes and cytotoxic for a wide range of tumor cells in vitro and in vivo.

Phenotypes From GWAS Catalog for LTA Gene

Gene Ontology (GO) - Molecular Function for LTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding TAS 3001529
GO:0005125 cytokine activity IEA --
GO:0005164 tumor necrosis factor receptor binding IEA --
genes like me logo Genes that share ontologies with LTA: view
genes like me logo Genes that share phenotypes with LTA: view

Animal Models for LTA Gene

MGI Knock Outs for LTA:

Animal Model Products

miRNA for LTA Gene

miRTarBase miRNAs that target LTA

Clone Products

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

Localization for LTA Gene

Subcellular locations from UniProtKB/Swiss-Prot for LTA Gene

Secreted. Membrane. Note=The homotrimer is secreted. The heterotrimer is membrane-associated.

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 LTA gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytosol 2
nucleus 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with LTA: view

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

Pathways & Interactions for LTA Gene

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

SIGNOR curated interactions for LTA Gene

Activates:

Gene Ontology (GO) - Biological Process for LTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEA --
GO:0002876 positive regulation of chronic inflammatory response to antigenic stimulus IEA --
GO:0002925 positive regulation of humoral immune response mediated by circulating immunoglobulin IEA --
GO:0006915 apoptotic process TAS 6334807
GO:0006955 immune response IEA --
genes like me logo Genes that share ontologies with LTA: view

Drugs & Compounds for LTA Gene

(35) Drugs for LTA Gene - From: DrugBank, PharmGKB, DGIdb, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Etanercept Approved, Investigational Pharma Target 413
Abacavir Approved, Investigational Pharma 222
Carbamazepine Approved, Investigational Pharma 134
BAMINERCEPT Pharma 0

(29) Additional Compounds for LTA Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LTA: view

Transcripts for LTA Gene

Unigene Clusters for LTA Gene

Lymphotoxin alpha (TNF superfamily, member 1):
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for LTA Gene

GeneLoc Exon Structure for
LTA
ECgene alternative splicing isoforms for
LTA

Expression for LTA Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of LTA Gene:

LTA

SOURCE GeneReport for Unigene cluster for LTA Gene:

Hs.36

Evidence on tissue expression from TISSUES for LTA Gene

  • Blood(3.2)
  • Spleen(2)
genes like me logo Genes that share expression patterns with LTA: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LTA Gene

Orthologs for LTA Gene

This gene was present in the common ancestor of chordates.

Orthologs for LTA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LTA 33 34
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia LTA 33 34
  • 83.5 (n)
cow
(Bos Taurus)
Mammalia LTA 33 34
  • 82.03 (n)
mouse
(Mus musculus)
Mammalia Lta 33 16 34
  • 78.88 (n)
rat
(Rattus norvegicus)
Mammalia Lta 33
  • 78.88 (n)
oppossum
(Monodelphis domestica)
Mammalia LTA 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lta 33
  • 46.15 (n)
zebrafish
(Danio rerio)
Actinopterygii tnfa 34
  • 25 (a)
ManyToMany
tnfb 34
  • 24 (a)
ManyToMany
Species where no ortholog for LTA 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LTA Gene

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

Paralogs for LTA Gene

Paralogs for LTA Gene

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

Variants for LTA Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for LTA Gene

TNFB_HUMAN-P01374
A polymorphism in LTA accounts, in part, for susceptibility to leprosy linked to chromosome 6p21.3 (LPRS4) [MIM:610988].

Sequence variations from dbSNP and Humsavar for LTA Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1041981 risk-factor, Myocardial infarction 31,573,007(+) C/A coding_sequence_variant, missense_variant
rs1799724 risk-factor, Vascular dementia, susceptibility to, Alzheimer disease, susceptibility to 31,574,705(+) C/T downstream_transcript_variant
rs2239704 risk-factor, Leprosy, early-onset, susceptibility to 31,572,364(+) A/C 5_prime_UTR_variant, intron_variant
rs879567734 risk-factor, Leprosy, early-onset, susceptibility to 31,572,364(+) A/ 5_prime_UTR_variant, intron_variant
rs909253 risk-factor, Myocardial infarction, Psoriatic arthritis, susceptibility to 31,572,536(+) A/G intron_variant

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

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
esv2759414 CNV gain+loss 17122850
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv462870 CNV loss 19166990
nsv470809 CNV loss 18288195
nsv601941 CNV loss 21841781
nsv830627 CNV loss 17160897

Variation tolerance for LTA Gene

Residual Variation Intolerance Score: 79.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.26; 96.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LTA Gene

Human Gene Mutation Database (HGMD)
LTA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LTA

SNP Genotyping and Copy Number Assay Products

Disorders for LTA Gene

MalaCards: The human disease database

(40) MalaCards diseases for LTA Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
psoriatic arthritis
  • psoriatic arthritis, susceptibility to
leprosy 4
  • leprosy, susceptibility to, 4
myocardial infarction
  • myocardial infarction, susceptibility to
acute respiratory distress syndrome
  • adult respiratory distress syndrome
transient hypogammaglobulinemia
- elite association - COSMIC cancer census association via MalaCards
Search LTA in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TNFB_HUMAN
  • Psoriatic arthritis (PSORAS) [MIM:607507]: An inflammatory, seronegative arthritis associated with psoriasis. It is a heterogeneous disorder ranging from a mild, non-destructive disease to a severe, progressive, erosive arthropathy. Five types of psoriatic arthritis have been defined: asymmetrical oligoarthritis characterized by primary involvement of the small joints of the fingers or toes; asymmetrical arthritis which involves the joints of the extremities; symmetrical polyarthritis characterized by a rheumatoid like pattern that can involve hands, wrists, ankles, and feet; arthritis mutilans, which is a rare but deforming and destructive condition; arthritis of the sacroiliac joints and spine (psoriatic spondylitis). {ECO:0000269 PubMed:12746914}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for LTA

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 LTA: view

No data available for Genatlas for LTA Gene

Publications for LTA Gene

  1. Association of LT-alpha Ala252Gly gene polymorphism and the genetic predisposition of coronary heart disease in Chinese. (PMID: 19365711) Gao H … Bai M (Molecular biology reports 2010) 3 22 44 58
  2. [Relationship between tumor necrosis factor beta gene polymorphism and acute respiratory distress syndrome after operation for esophageal carcinoma]. (PMID: 19958618) Liu LX … Hu ZJ (Ai zheng = Aizheng = Chinese journal of cancer 2009) 3 22 44 58
  3. Genetic variation in TNF and IL10 and risk of non-Hodgkin lymphoma: a report from the InterLymph Consortium. (PMID: 16389181) Rothman N … Nieters A (The Lancet. Oncology 2006) 3 22 44 58
  4. Genetic impact of TNF-beta on risk factors for coronary atherosclerosis. (PMID: 17194634) Schulz S … Gläser C (European cytokine network 2006) 3 22 44 58
  5. Functional variants in the lymphotoxin-alpha gene predict cardiovascular disease in dialysis patients. (PMID: 16988060) Liu Y … Coresh J (Journal of the American Society of Nephrology : JASN 2006) 3 22 44 58

Products for LTA Gene

Sources for LTA Gene

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