LTA (Lymphotoxin-A)

2005-02-01 Fei Chen Affiliation

Health Effects Laboratory Division, NIOSH, 1095 Willowdale Rd, Morgantown, WV 26505, USA

Identity

HGNC

LTA

LOCATION

6p21.33

LOCUSID

4049

ALIAS

LT,TNFB,TNFSF1,TNLG1E

DNA/RNA

Description

The human TNFb gene is located next to HLA-C and HLA-B loci in chromosome 6 (6p21.3). The gene spans 2005bp with 4 exons, which transcribes a TNFb mRNA with size of 1386nt.

Proteins

Description

The human TNFb protein contains 205 amino acids. The soluble form of TNFb is usually a homotrimer with a relative molecular mass of 60 to 70 kDa, whereas the membrane form of TNFb is a heteromeric complex with lymphotoxin b (TNFc, LTb, TNFSF3). The human TNFb shares 35% identity and 50% homology in amino acid sequence with the human TNFa. The biological function of TNFb is mediated largely by TNFa receptor 1 and TNFa receptor 2. Recent studies suggested that TNFb can also recognize LIGHT ( TNFSF14) receptor.

Expression

The main cellular source of TNFb is the activated lymphocytes in immune response.

Localisation

Cell membrane, extracellular soluble form, blood stream, and biological fluids.

Function

The human TNFb is an important cytokine involved in the development of secondary lymphoid organs and inflammatory responses.

Implicated in

Disease

The polymorphism of TNFb gene in either the coding region or the promoter region has been associated with Crohn disease and myocardial infarction.

Article Bibliography

Pubmed ID	Last Year	Title	Authors
12949498	2003	Signalling pathways of the TNF superfamily: a double-edged sword.	Aggarwal BB et al
12974479	2003	Lymphotoxin/light, lymphoid microenvironments and autoimmune disease.	Gommerman JL et al

Other Information

Locus ID:

NCBI: 4049
MIM: 153440
HGNC: 6709
Ensembl: ENSG00000226979

Variants:

dbSNP: 4049
ClinVar: 4049
TCGA: ENSG00000226979
COSMIC: LTA

RNA/Proteins

Gene ID	Transcript ID	Uniprot
ENSG00000226979	ENST00000418386	P01374
ENSG00000226979	ENST00000418386	Q5STV3
ENSG00000226979	ENST00000454783	P01374
ENSG00000226979	ENST00000454783	Q5STV3

Expression (GTEx)

100

150

200

250

300

350

Adipose - Subcutaneous

Adipose - Visceral

Adrenal Gland

Artery - Aorta

Artery - Tibial

Bladder

Brain - Amygdala

Brain - Anterior cingulate cortex

Brain - Caudate

Brain - Cerebellar Hemisphere

Brain - Cerebellum

Brain - Cortex

Brain - Frontal Cortex

Brain - Hippocampus

Brain - Hypothalamus

Brain - Nucleus accumbens

Brain - Putamen

Brain - Spinal cord

Brain - Substantia nigra

Breast - Mammary Tissue

Cells - Cultured fibroblasts

Cells - EBV - transformed lymphocytes

Cervix - Ectocervix

Cervix - Endocervix

Colon - Sigmoid

Colon - Transverse

Esophagus - Gastroesophageal Junction

Esophagus - Mucosa

Esophagus - Muscularis

Fallopian Tube

Heart - Atrial Appendage

Heart - Left Ventricle

Kidney - Cortex

Kidney - Medulla

Liver

Lung

Minor Salivary Gland

Muscle - Skeletal

Nerve - Tibial

Ovary

Pancreas

Pituitary

Prostate

Skin - Not Sun Exposed

Skin - Sun Exposed

Small Intestine - Terminal Ileum

Spleen

Stomach

Testis

Thyroid

Uterus

Vagina

Whole Blood

Pathways

Pathway	Source	External ID
Cytokine-cytokine receptor interaction	KEGG	ko04060
Type I diabetes mellitus	KEGG	ko04940
Cytokine-cytokine receptor interaction	KEGG	hsa04060
Type I diabetes mellitus	KEGG	hsa04940
HTLV-I infection	KEGG	ko05166
HTLV-I infection	KEGG	hsa05166
Herpes simplex infection	KEGG	ko05168
Herpes simplex infection	KEGG	hsa05168
NF-kappa B signaling pathway	KEGG	hsa04064
NF-kappa B signaling pathway	KEGG	ko04064
TNF signaling pathway	KEGG	hsa04668
TNF signaling pathway	KEGG	ko04668
Immune System	REACTOME	R-HSA-168256
Cytokine Signaling in Immune system	REACTOME	R-HSA-1280215
TNFR2 non-canonical NF-kB pathway	REACTOME	R-HSA-5668541
TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway	REACTOME	R-HSA-5676594
TNFs bind their physiological receptors	REACTOME	R-HSA-5669034

Protein levels (Protein atlas)

Not detected

Low

Medium

High

PharmGKB

Entity ID	Name	Type	Evidence	Association	PD	PMIDs
PA443936	Drug Hypersensitivity	Disease	ClinicalAnnotation	associated	PD
PA444546	Hypersensitivity	Disease	ClinicalAnnotation	associated	PD	11294926
PA448004	abacavir	Chemical	ClinicalAnnotation	associated	PD
PA448785	carbamazepine	Chemical	ClinicalAnnotation	associated	PD	11294926

References

Pubmed ID	Year	Title	Citations
36802017	2023	Combined tumor necrosis factor-α (-308 G/A) and tumor necrosis factor-β (+ 252 A/G) nucleotide polymorphisms and chronicity in Egyptian children with immune thrombocytopenia.	0
36929286	2023	Prognostic significance of the genetic variant of lymphotoxin alpha (p.Thr60Asn) in egyptian patients with advanced hepatocellular carcinoma.	0
36802017	2023	Combined tumor necrosis factor-α (-308 G/A) and tumor necrosis factor-β (+ 252 A/G) nucleotide polymorphisms and chronicity in Egyptian children with immune thrombocytopenia.	0
36929286	2023	Prognostic significance of the genetic variant of lymphotoxin alpha (p.Thr60Asn) in egyptian patients with advanced hepatocellular carcinoma.	0
33779868	2022	Genetic polymorphism of tumor necrosis factor alpha (TNF-α) and tumor necrosis factor beta (TNF-β) genes and risk of oral pre-cancer and cancer in North Indian population.	3
36430258	2022	Association of LTA and SOD Gene Polymorphisms with Cerebral White Matter Hyperintensities in Migraine Patients.	2
33779868	2022	Genetic polymorphism of tumor necrosis factor alpha (TNF-α) and tumor necrosis factor beta (TNF-β) genes and risk of oral pre-cancer and cancer in North Indian population.	3
36430258	2022	Association of LTA and SOD Gene Polymorphisms with Cerebral White Matter Hyperintensities in Migraine Patients.	2
31928491	2021	Genetic Variation on TNF/LTA and TNFRSF1A Genes is Associated with Outcomes of Hepatitis C Virus Infection.	5
33433759	2021	Association between tumor necrosis factor alpha and lymphotoxin alpha gene polymorphisms and migraine occurrence among Jordanians.	7
33436266	2021	Genetic variants in TNFA, LTA, TLR2 and TLR4 genes and risk of sepsis in patients with severe trauma: nested case-control study in a level-1 trauma centre in SERBIA.	2
33441130	2021	Elevated lymphotoxin-α (TNFβ) is associated with intervertebral disc degeneration.	2
34595982	2021	Polymorphisms of the TNF, LTA, and TNFRSF1B genes are associated with onsets of menarche and menopause in US women of European ancestry.	0
31928491	2021	Genetic Variation on TNF/LTA and TNFRSF1A Genes is Associated with Outcomes of Hepatitis C Virus Infection.	5
33433759	2021	Association between tumor necrosis factor alpha and lymphotoxin alpha gene polymorphisms and migraine occurrence among Jordanians.	7

Citation

Fei Chen

LTA (Lymphotoxin-A)

Atlas Genet Cytogenet Oncol Haematol. 2005-02-01

Online version: http://atlasgeneticsoncology.org/gene/41209/lta-(lymphotoxin-a)