Gene:
LTA
lymphotoxin alpha (TNF superfamily, member 1)

PharmGKB contains no dosing guidelines for this . To report known genotype-based dosing guidelines, or if you are interested in developing guidelines, click here.

PharmGKB has no annotated drug labels with pharmacogenomic information for this . If you know of a drug label with PGx, send us a message.

PharmGKB contains no Clinical Variants that meet the highest level of criteria.

To see more Clinical Variants with lower levels of criteria, click the button at the bottom of the table.

Disclaimer: The PharmGKB's clinical annotations reflect expert consensus based on clinical evidence and peer-reviewed literature available at the time they are written and are intended only to assist clinicians in decision-making and to identify questions for further research. New evidence may have emerged since the time an annotation was submitted to the PharmGKB. The annotations are limited in scope and are not applicable to interventions or diseases that are not specifically identified.

The annotations do not account for individual variations among patients, and cannot be considered inclusive of all proper methods of care or exclusive of other treatments. It remains the responsibility of the health-care provider to determine the best course of treatment for a patient. Adherence to any guideline is voluntary, with the ultimate determination regarding its application to be made solely by the clinician and the patient. PharmGKB assumes no responsibility for any injury or damage to persons or property arising out of or related to any use of the PharmGKB clinical annotations, or for any errors or omissions.

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This is a non-comprehensive list of genetic tests with pharmacogenetics relevance, typically submitted by the manufacturer and manually curated by PharmGKB. The information listed is provided for educational purposes only and does not constitute an endorsement of any listed test or manufacturer.

A more complete listing of genetic tests is found at the Genetic Testing Registry (GTR).

PGx Test Variants Assayed Related Drugs?

The table below contains information about pharmacogenomic variants on PharmGKB. Please follow the link in the "Variant" column for more information about a particular variant. Each link in the "Variant" column leads to the corresponding PharmGKB Variant Page. The Variant Page contains summary data, including PharmGKB manually curated information about variant-drug pairs based on individual PubMed publications. The PMIDs for these PubMed publications can be found on the Variant Page.

The tags in the first column of the table indicate what type of information can be found on the corresponding Variant Page on the appropriate tab.

Links in the "Drugs" column lead to PharmGKB Drug Pages.

List of all LTA variant annotations

Variant?
(142)
Alternate Names ? Drugs ? Alleles ?
(+ chr strand)
Function ? Amino Acid?
Translation
No VIP available No Clinical Annotations available VA
rs1041981 179C>A, 2435C>A, 2826325C>A, 2834422C>A, 2871585C>A, 2883668C>A, 2920490C>A, 3050400A>A, 31480784C>A, 31540784C>A, 5909C>A
C > A
Missense
Thr60Asn
No VIP available CA VA
rs1800629 -308, -308G>A, -488G>A, 2828572G>A, 2836669G>A, 2873832G>A, 2885915G>A, 2922737G>A, 3052647A>A, 31483031G>A, 31543031G>A, 4682G>A, 8156G>A, TNF alpha -308G/A, TNF2, TNF:, TNF:-308 G/A, TNF:-308G/A
G > A
5' Flanking
No VIP available No Clinical Annotations available VA
rs3093726 2832330C>C, 2840429T>C, 2861507T>C, 2877590T>C, 2889673T>C, 2926495T>C, 3056405T>C, 31486789T>C, 31546789T>C, 8440T>C
T > C
Not Available
No VIP available No Clinical Annotations available VA
rs909253 -10+90A>G, -9-198A>G, 115+47T>C, 1964A>G, 2825852A>G, 2833949A>G, 2871114A>G, 2883197A>G, 2920017A>G, 3049929G>G, 31480313A>G, 31540313A>G, 5438A>G, G/A, intron 1 c.-10+90
A > G
Intronic
Alleles, Functions, and Amino Acid Translations are all sourced from dbSNP 142

Overview

Alternate Names:  TNF superfamily member 1; TNFB; lymphotoxin alpha (TNF superfamily, member 1)
Alternate Symbols:  LT; TNFSF1
PharmGKB Accession Id: PA30474

Details

Cytogenetic Location: chr6 : p21.33 - p21.33
GP mRNA Boundary: chr6 : 31539876 - 31542098
GP Gene Boundary: chr6 : 31529876 - 31545098
Strand: plus
The mRNA boundaries are calculated using the gene's default feature set from NCBI, mapped onto the UCSC Golden Path. PharmGKB sets gene boundaries by expanding the mRNA boundaries by no less than 10,000 bases upstream (5') and 3,000 bases downstream (3') to allow for potential regulatory regions.

PharmGKB Curated Pathways

Pathways created internally by PharmGKB based primarily on literature evidence.

PharmGKB contains no curated pathways for this gene. If you would like to volunteer to work on a pathway, please let us know.

External Pathways

Links to non-PharmGKB pathways.

  1. IL2 signaling events mediated by STAT5 - (Pathway Interaction Database NCI-Nature Curated)
  2. IL4-mediated signaling events - (Pathway Interaction Database NCI-Nature Curated)
  3. tnfr2 signaling pathway - (BioCarta via Pathway Interaction Database)
No related genes are available

Curated Information ?

Curated Information ?

Publications related to LTA: 16

No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
Pharmacogenetics of disease-modifying antirheumatic drugs in rheumatoid arthritis: towards personalized medicine. Pharmacogenomics. 2013. Umićević Mirkov Maša, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available VA No VIP available No VIP available
TGF beta1 polymorphisms are candidate predictors of the clinical response to rituximab in rheumatoid arthritis. Joint, bone, spine : revue du rhumatisme. 2012. Daïen Claire Immediato, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
A large-scale candidate gene approach identifies SNPs in SOD2 and IL13 as predictive markers of response to preoperative chemoradiation in rectal cancer. The pharmacogenomics journal. 2010. Ho-Pun-Cheung A, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
The TNF superfamily in 2009: new pathways, new indications, and new drugs. Drug discovery today. 2009. Tansey Malú G, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
TP53 R72P and MDM2 SNP309 polymorphisms in modification of childhood acute lymphoblastic leukemia susceptibility. Cancer genetics and cytogenetics. 2009. Do Thuy N, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available VA No VIP available No VIP available
TNF-alpha-308 G/A polymorphism and responsiveness to TNF-alpha blockade therapy in moderate to severe rheumatoid arthritis: a systematic review and meta-analysis. The pharmacogenomics journal. 2009. O'Rielly D D, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
TNF, LTA, HSPA1L and HLA-DR gene polymorphisms in HIV-positive patients with hypersensitivity to cotrimoxazole. Pharmacogenomics. 2009. Alfirevic Ana, et al. PubMed
No Dosing Guideline available No Drug Label available CA No Variant Annotation available No VIP available No VIP available
Association of four DNA polymorphisms with acute rejection after kidney transplantation. Transplant international : official journal of the European Society for Organ Transplantation. 2008. Grinyó Josep, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
STAT3 polymorphism predicts interferon-alfa response in patients with metastatic renal cell carcinoma. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2007. Ito Noriyuki, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
Stepwise replication identifies a low-producing lymphotoxin-alpha allele as a major risk factor for early-onset leprosy. Nature genetics. 2007. Alcaïs Alexandre, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
Lymphotoxin beta receptor-dependent control of lipid homeostasis. Science (New York, N.Y.). 2007. Lo James C, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available VA No VIP available No VIP available
A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nature genetics. 2006. de Bakker Paul I W, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
The influence of genetic variation in the HLA-DRB1 and LTA-TNF regions on the response to treatment of early rheumatoid arthritis with methotrexate or etanercept. Arthritis and rheumatism. 2004. Criswell Lindsey A, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
ANCA pattern and LTA haplotype relationship to clinical responses to anti-TNF antibody treatment in Crohn's disease. Gastroenterology. 2001. Taylor K D, et al. PubMed
No Dosing Guideline available No Drug Label available CA VA No VIP available No VIP available
TNFalpha promoter region gene polymorphisms in carbamazepine-hypersensitive patients. Neurology. 2001. Pirmohamed M, et al. PubMed
No Dosing Guideline available No Drug Label available No Clinical Annotation available No Variant Annotation available No VIP available No VIP available
Relation of a TNF gene polymorphism to severe sepsis in trauma patients. Annals of surgery. 1999. Majetschak M, et al. PubMed

LinkOuts

HuGE:
LTA
Comparative Toxicogenomics Database:
4049
ModBase:
P01374
HumanCyc Gene:
HS10676
HGNC:
6709

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