TSPO

translocator protein

Basic information

Region (hg38): 22:43151546-43163242

Previous symbols: [ "BZRP" ]

Links

ENSG00000100300 ∙ NCBI:706 ∙ OMIM:109610 ∙ HGNC:1158 ∙ Uniprot:B1AH88, P30536 ∙ 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 TSPO gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	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)
22-43159399-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)
22-43162939-G-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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