TSPO
protein-codingtranslocator protein
Gene summary
Present mainly in the mitochondrial compartment of peripheral tissues, the protein encoded by this gene interacts with some benzodiazepines and has different affinities than its endogenous counterpart. The protein is a key factor in the flow of cholesterol into mitochondria to permit the initiation of steroid hormone synthesis. Alternatively spliced transcript variants have been reported; one of the variants lacks an internal exon and is considered non-coding, and the other variants encode the same protein. [provided by RefSeq, Feb 2012]
- BZRP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TSPO variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000714.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | 6 | ||||
| missense | 13 | 2 | 15 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 13 | 8 | 0 | 21 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000705.2 | 3 | MANE Select | |
| Ensembl | ENSP00000338004.3 | 3 | MANE Select | |
| RefSeq | NP_001243459.1 | 3 | Standard | |
| RefSeq | NP_001243460.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| tspo | Danio rerio | Structure: nucleate erythrocyte Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
Biological Process
- protein targeting to mitochondrion
- C21-steroid hormone biosynthetic process
- heme biosynthetic process
- anion transport
- chloride transport
Molecular Function
- androgen binding
- protein binding
- benzodiazepine receptor activity
- cholesterol binding
- cholesterol transporter activity
Cellular Component
- mitochondrial outer membrane
- endoplasmic reticulum
- integral component of membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000329563
- Coding exons
- 3
- Length
- 11729
- Individuals with no LoFs
- 125590
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125596
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.956 | 70 | 96.4 | 0.726 | 0.00000621 | 1016 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000059 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.259
Intolerance Scores
- LoFtool
- 0.300
- RVIS EVS
- 0.73
- RVIS percentile EVS
- 85.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.489
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |