LTB

lymphotoxin beta, the group of Tumor necrosis factor superfamily

Basic information

Region (hg38): 6:31580525-31582522

Previous symbols: [ "TNFC" ]

Links

ENSG00000227507

∙ NCBI:4050 ∙ OMIM:600978 ∙ HGNC:6711 ∙ Uniprot:Q06643 ∙ 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 LTB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTB 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			1 clinvar	1 clinvar	2 clinvar	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	2

Variants in LTB

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

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

Position	Phenotype	Significance	ClinVar
6-31580924-T-G	not specified	Uncertain significance (Jul 17, 2024)	3540997
6-31580980-C-G	not specified	Likely benign (Jan 23, 2024)	3121378
6-31580990-G-T	not specified	Uncertain significance (Nov 10, 2024)	3540998
6-31581079-G-A		Benign (Dec 31, 2019)	770169
6-31581580-G-A		Benign (Dec 31, 2019)	778228
6-31581611-C-T	not specified	Likely benign (Dec 10, 2024)	3540996
6-31581828-G-T	not specified	Uncertain significance (Oct 26, 2021)	2257421

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTB	protein_coding	protein_coding	ENST00000429299	4	1998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.61e-11	0.0123	123484	0	17	123501	0.0000688

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.787	111	137	0.811	0.00000647	1474
Missense in Polyphen		26	53.062	0.48999		560
Synonymous	-0.0517	70	69.5	1.01	0.00000369	557
Loss of Function	-1.26	13	8.95	1.45	3.82e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000590	0.0000590
Ashkenazi Jewish	0.000104	0.000100
East Asian	0.0000548	0.0000547
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000925	0.0000902
Middle Eastern	0.0000548	0.0000547
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Cytokine that binds to LTBR/TNFRSF3. May play a specific role in immune response regulation. Provides the membrane anchor for the attachment of the heterotrimeric complex to the cell surface. Isoform 2 is probably non-functional.;
Pathway: Rheumatoid arthritis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Spinal Cord Injury;EDA Signalling in Hair Follicle Development;TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System (Consensus)

Intolerance Scores

loftool: 0.404
rvis_EVS: 0.37
rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

pHI: 0.129
hipred: N
hipred_score: 0.294
ghis: 0.446

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.879

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ltb
Phenotype: immune system phenotype; vision/eye 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); digestive/alimentary 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); hematopoietic system phenotype; respiratory system phenotype; liver/biliary system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: immune response;signal transduction;cell-cell signaling;gene expression;regulation of signaling receptor activity;tumor necrosis factor-mediated signaling pathway;skin development;positive regulation of interleukin-12 biosynthetic process;lymph node development
Cellular component: cellular_component;extracellular space;plasma membrane;integral component of membrane
Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding