LTBR

lymphotoxin beta receptor, the group of Tumor necrosis factor receptor superfamily

Basic information

Region (hg38): 12:6375044-6391571

Previous symbols: [ "D12S370" ]

Links

ENSG00000111321 ∙ NCBI:4055 ∙ OMIM:600979 ∙ HGNC:6718 ∙ Uniprot:P36941 ∙ 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 LTBR gene.

• Inborn genetic diseases (17 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTBR 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					5	5
missense			15	2	3	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	15	2	9

Variants in LTBR

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

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

Position	Type	Phenotype	Significance	ClinVar
12-6375164-T-C			Likely benign (Oct 02, 2019)
12-6375500-C-G		Bronchiectasis with or without elevated sweat chloride 2 • Autosomal recessive pseudohypoaldosteronism type 1 • SCNN1A-related disorder	Benign (May 22, 2019)
12-6375503-A-G		Autosomal recessive pseudohypoaldosteronism type 1 • Bronchiectasis with or without elevated sweat chloride 2	Conflicting classifications of pathogenicity (Jul 31, 2019)
12-6375509-C-G		Bronchiectasis with or without elevated sweat chloride 2 • Autosomal recessive pseudohypoaldosteronism type 1	Uncertain significance (Jan 12, 2018)
12-6375519-G-A		Autosomal recessive pseudohypoaldosteronism type 1 • Bronchiectasis with or without elevated sweat chloride 2	Benign/Likely benign (Jan 13, 2018)
12-6375543-T-C		Bronchiectasis with or without elevated sweat chloride 2 • Autosomal recessive pseudohypoaldosteronism type 1	Benign (Jan 13, 2018)
12-6375605-C-T		Autosomal recessive pseudohypoaldosteronism type 1 • Bronchiectasis with or without elevated sweat chloride 1	Likely benign (May 22, 2021)
12-6375606-G-A		Autosomal recessive pseudohypoaldosteronism type 1 • Bronchiectasis with or without elevated sweat chloride 1	Likely benign (Jun 14, 2016)
12-6375636-G-A		Autosomal recessive pseudohypoaldosteronism type 1 • Bronchiectasis with or without elevated sweat chloride 1	Likely benign (Jun 14, 2016)
12-6377358-T-C			Benign (Sep 19, 2020)
12-6377490-T-C			Benign (Sep 04, 2018)
12-6384393-T-A		not specified	Uncertain significance (Nov 08, 2022)
12-6384410-G-A		not specified	Uncertain significance (Jan 04, 2024)
12-6384579-C-T			Benign (Dec 31, 2019)
12-6384647-G-A			Benign (Jan 05, 2018)
12-6384651-C-G		not specified	Uncertain significance (Jun 13, 2023)
12-6384672-C-T		not specified	Uncertain significance (Oct 06, 2022)
12-6385049-G-A		not specified	Uncertain significance (Dec 22, 2023)
12-6385074-A-G			Benign (Jun 23, 2018)
12-6385280-C-G		not specified	Uncertain significance (Feb 03, 2022)
12-6385291-G-A			Benign (Jun 05, 2018)
12-6385344-C-T			Benign (Jul 06, 2018)
12-6386133-C-T			Benign (Jun 05, 2018)
12-6386159-C-G		not specified	Uncertain significance (Dec 17, 2021)
12-6386402-A-G		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTBR	protein_coding	protein_coding	ENST00000228918	10	16523

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.306	0.694	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.03	166	258	0.643	0.0000151	2777
Missense in Polyphen		29	86.015	0.33715		966
Synonymous	0.635	105	114	0.924	0.00000758	899
Loss of Function	3.29	5	21.4	0.234	9.17e-7	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the heterotrimeric lymphotoxin containing LTA and LTB, and for TNFS14/LIGHT. Promotes apoptosis via TRAF3 and TRAF5. May play a role in the development of lymphoid organs. {ECO:0000269|PubMed:10799510, ECO:0000269|PubMed:8171323}.
• Pathway: HIF-1 signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Busulfan Pathway, Pharmacodynamics;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)

Recessive Scores

• pRec: 0.531

Intolerance Scores

• loftool: 0.178
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.340
• hipred: Y
• hipred_score: 0.594
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.286

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ltbr
• Phenotype: hematopoietic system phenotype; normal 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); immune system phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: apoptotic process;immune response;signal transduction;viral process;tumor necrosis factor-mediated signaling pathway;myeloid dendritic cell differentiation;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of JNK cascade;cellular response to mechanical stimulus;positive regulation of extrinsic apoptotic signaling pathway
• Cellular component: Golgi apparatus;plasma membrane;integral component of membrane
• Molecular function: protein binding;ubiquitin protein ligase binding;identical protein binding