TNFRSF17
Basic information
Region (hg38): 16:11965210-11968068
Previous symbols: [ "BCMA" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (21 variants)
- not_provided (3 variants)
- Desmoplastic_small_round_cell_tumor (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF17 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001192.3. 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 | 0 | |||||
| missense | 24 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 24 | 0 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TNFRSF17 | protein_coding | protein_coding | ENST00000053243 | 3 | 2962 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000137 | 0.124 | 125700 | 0 | 48 | 125748 | 0.000191 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.24 | 143 | 107 | 1.34 | 0.00000591 | 1206 |
| Missense in Polyphen | 34 | 31.693 | 1.0728 | 362 | ||
| Synonymous | -1.12 | 51 | 41.8 | 1.22 | 0.00000261 | 353 |
| Loss of Function | -0.626 | 8 | 6.30 | 1.27 | 3.28e-7 | 83 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000179 | 0.000179 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.000979 | 0.000979 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000159 | 0.000158 |
| Middle Eastern | 0.000979 | 0.000979 |
| South Asian | 0.000197 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for TNFSF13B/BLyS/BAFF and TNFSF13/APRIL. Promotes B-cell survival and plays a role in the regulation of humoral immunity. Activates NF-kappa-B and JNK. {ECO:0000269|PubMed:10801128, ECO:0000269|PubMed:10903733, ECO:0000269|PubMed:10973284}.;
- Pathway
- Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);yaci and bcma stimulation of b cell immune responses;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors
(Consensus)
Recessive Scores
- pRec
- 0.284
Intolerance Scores
- loftool
- 0.689
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 68.13
Haploinsufficiency Scores
- pHI
- 0.106
- hipred
- N
- hipred_score
- 0.213
- ghis
- 0.525
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.833
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tnfrsf17
- Phenotype
- normal phenotype; reproductive system phenotype; 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; immune system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- adaptive immune response;lymphocyte homeostasis;signal transduction;multicellular organism development;cell population proliferation;tumor necrosis factor-mediated signaling pathway
- Cellular component
- plasma membrane;endomembrane system;integral component of membrane
- Molecular function
- signaling receptor activity