TSPO2

translocator protein 2

Basic information

Region (hg38): 6:41042466-41044337

Previous symbols: [ "BZRPL1" ]

Links

ENSG00000112212 ∙ NCBI:222642 ∙ OMIM:619409 ∙ HGNC:21256 ∙ Uniprot:Q5TGU0 ∙ 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 TSPO2 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPO2 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			4	2		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	2	0

Variants in TSPO2

This is a list of pathogenic ClinVar variants found in the TSPO2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-41043007-T-G		not specified	Uncertain significance (Sep 17, 2021)
6-41043055-C-T		not specified	Uncertain significance (Jun 18, 2021)
6-41043056-G-A		not specified	Likely benign (Nov 12, 2021)
6-41043092-T-A		not specified	Likely benign (Jan 18, 2023)
6-41044052-C-T		not specified	Uncertain significance (Aug 17, 2022)
6-41044124-A-G		not specified	Uncertain significance (Dec 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPO2	protein_coding	protein_coding	ENST00000373161	3	1784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000899	0.585	125728	1	19	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.550	75	89.6	0.837	0.00000455	1059
Missense in Polyphen		19	30.052	0.63224		427
Synonymous	0.510	38	42.2	0.900	0.00000214	381
Loss of Function	0.473	5	6.28	0.796	2.68e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000994	0.0000653
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds cholesterol and mediates its redistribution during erythropoiesis which may play a role in erythrocyte maturation. {ECO:0000269|PubMed:19729679}.

Recessive Scores

• pRec: 0.0822

Intolerance Scores

• loftool: 0.786
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.34

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tspo2

Gene ontology

• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: cholesterol binding