LTBR
Basic information
Region (hg38): 12:6375045-6391571
Previous symbols: [ "D12S370" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 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. These statistics are base on transcript: NM_000002342.3. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | |||||
| missense | 47 | 55 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 47 | 5 | 8 |
GnomAD
Source:
| 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:
- 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