TSPO
translocator protein
Basic information
Region (hg38): 22:43151547-43163242
Previous symbols: [ "BZRP" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPO 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 0 |
Variants in TSPO
This is a list of pathogenic ClinVar variants found in the TSPO region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-43159279-C-T | Likely benign (Jul 29, 2018) | |||
| 22-43159309-G-A | not specified | Uncertain significance (Sep 28, 2022) | ||
| 22-43159333-G-A | not specified | Uncertain significance (Jun 28, 2024) | ||
| 22-43159399-G-A | not specified | Uncertain significance (Oct 03, 2023) | ||
| 22-43159413-G-A | not specified | Uncertain significance (Jul 26, 2022) | ||
| 22-43161084-G-A | not specified | Uncertain significance (Aug 21, 2023) | ||
| 22-43161164-T-G | not specified | Uncertain significance (Jun 11, 2021) | ||
| 22-43161165-T-C | not specified | Uncertain significance (Apr 18, 2023) | ||
| 22-43162864-A-T | not specified | Uncertain significance (Mar 21, 2023) | ||
| 22-43162892-C-G | not specified | Likely benign (May 30, 2024) | ||
| 22-43162939-G-A | not specified | Uncertain significance (Aug 08, 2022) | ||
| 22-43162956-C-T | not specified | Uncertain significance (Sep 26, 2024) | ||
| 22-43162957-A-G | not specified | Likely benign (Mar 19, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TSPO | protein_coding | protein_coding | ENST00000329563 | 3 | 11729 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000274 | 0.569 | 125590 | 0 | 6 | 125596 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.956 | 70 | 96.4 | 0.726 | 0.00000621 | 1016 |
| Missense in Polyphen | 20 | 29.633 | 0.67493 | 393 | ||
| Synonymous | 0.122 | 43 | 44.0 | 0.977 | 0.00000290 | 365 |
| Loss of Function | 0.533 | 6 | 7.59 | 0.791 | 4.14e-7 | 68 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000120 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Benzodiazepine Pathway, Pharmacodynamics;HTLV-I infection - Homo sapiens (human);Cholesterol metabolism - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);NO-cGMP-PKG mediated Neuroprotection;Metabolism of lipids;Metabolism;Pregnenolone biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Steroid hormones
(Consensus)
Recessive Scores
- pRec
- 0.259
Intolerance Scores
- loftool
- 0.300
- rvis_EVS
- 0.73
- rvis_percentile_EVS
- 85.98
Haploinsufficiency Scores
- pHI
- 0.200
- hipred
- N
- hipred_score
- 0.310
- ghis
- 0.408
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.489
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tspo
- Phenotype
- cellular phenotype; immune system phenotype; normal phenotype; hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- tspo
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- protein targeting to mitochondrion;C21-steroid hormone biosynthetic process;heme biosynthetic process;anion transport;chloride transport;apoptotic process;aging;steroid metabolic process;cell population proliferation;glial cell migration;response to manganese ion;response to vitamin B1;positive regulation of necrotic cell death;peripheral nervous system axon regeneration;cholesterol transport;adrenal gland development;negative regulation of protein ubiquitination;regulation of cholesterol transport;response to progesterone;negative regulation of tumor necrosis factor production;response to testosterone;positive regulation of apoptotic process;negative regulation of nitric oxide biosynthetic process;behavioral response to pain;regulation of steroid biosynthetic process;positive regulation of mitochondrial depolarization;positive regulation of calcium ion transport;contact inhibition;positive regulation of glial cell proliferation;negative regulation of glial cell proliferation;cellular response to lipopolysaccharide;cellular response to zinc ion;cellular hypotonic response;maintenance of protein location in mitochondrion;negative regulation of autophagy of mitochondrion;negative regulation of ATP metabolic process;positive regulation of reactive oxygen species metabolic process
- Cellular component
- mitochondrial outer membrane;endoplasmic reticulum;integral component of membrane;extracellular exosome
- Molecular function
- androgen binding;protein binding;benzodiazepine receptor activity;cholesterol binding;cholesterol transporter activity;ion channel binding