LTA

lymphotoxin alpha, the group of Tumor necrosis factor superfamily

Basic information

Region (hg38): 6:31572053-31574324

Previous symbols: [ "TNFB" ]

Links

ENSG00000226979 ∙ NCBI:4049 ∙ OMIM:153440 ∙ HGNC:6709 ∙ Uniprot:P01374 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LTA gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in LTA

This is a list of pathogenic ClinVar variants found in the LTA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-31572364-A-A		Leprosy, early-onset, susceptibility to	risk factor (Apr 01, 2007)
6-31572536-A-G		Psoriatic arthritis, susceptibility to • Myocardial infarction, susceptibility to	risk factor (Feb 15, 2004)
6-31572779-T-C		LTA-related disorder	Benign (Oct 17, 2019)
6-31572986-A-G		not specified	Uncertain significance (Dec 26, 2023)
6-31573006-A-G		not specified	Uncertain significance (Mar 07, 2023)
6-31573007-C-A		Myocardial infarction, susceptibility to • LTA-related disorder	Benign (Oct 16, 2019)
6-31573020-T-C		LTA-related disorder	Likely benign (Jul 12, 2019)
6-31573391-A-G		not specified	Uncertain significance (Jan 24, 2023)
6-31573400-G-A		not specified	Uncertain significance (Sep 25, 2023)
6-31573497-A-C		not specified	Uncertain significance (Dec 19, 2023)
6-31573586-G-A		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTA	protein_coding	protein_coding	ENST00000454783	3	2271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.197	0.762	125742	0	2	125744	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	60	115	0.524	0.00000598	1307
Missense in Polyphen		10	40.322	0.24801		478
Synonymous	1.44	37	49.9	0.741	0.00000266	457
Loss of Function	1.69	2	6.75	0.296	2.89e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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.
• Disease: DISEASE: 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.
• Pathway: Type I diabetes mellitus - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Apoptosis;Apoptotic Signaling Pathway;tnfr2 signaling pathway;TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;TNFs bind their physiological receptors;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i;IL2 signaling events mediated by STAT5;IL4-mediated signaling events (Consensus)

Intolerance Scores

• loftool: 0.133
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.316
• hipred: N
• hipred_score: 0.454
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.839

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Lta
• Phenotype: limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: response to hypoxia;positive regulation of chronic inflammatory response to antigenic stimulus;positive regulation of humoral immune response mediated by circulating immunoglobulin;apoptotic process;humoral immune response;signal transduction;cell-cell signaling;response to nutrient;regulation of signaling receptor activity;response to lipopolysaccharide;positive regulation of interferon-gamma production;tumor necrosis factor-mediated signaling pathway;response to drug;positive regulation of apoptotic process;negative regulation of growth of symbiont in host;negative regulation of fibroblast proliferation;lymph node development;defense response to Gram-positive bacterium;positive regulation of glial cell proliferation
• Cellular component: extracellular space;plasma membrane
• Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding