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.

• not_specified (16 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_000002341.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	1		2
missense			13	4	2	19
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	16	5	2

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
		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

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

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