TSPOAP1

TSPO associated protein 1, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 17:58301227-58328795

Previous symbols: [ "BZRAP1" ]

Links

ENSG00000005379 ∙ NCBI:9256 ∙ OMIM:610764 ∙ HGNC:16831 ∙ Uniprot:O95153 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• TH-deficient dopa-responsive dystonia (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Dystonia 22, juvenile-onset; Dystonia 22, adult-onset	AR	Neurologic	Individuals have been described as responding to some medications used to treat dystonia (eg, clonazepam, phenytoin), but not other medications, and awareness may enable tailored medical management	Neurologic	33539324

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPOAP1 gene.

• not provided (27 variants)
• Inborn genetic diseases (11 variants)
• not specified (4 variants)
• TSPOAP1-related Dystonia (2 variants)
• Bardet-Biedl syndrome (2 variants)
• TSPOAP1-related condition (1 variants)
• Dystonia 22, adult-onset (1 variants)
• Neurodevelopmental disorder (1 variants)
• Juvenile-onset progressive generalized dystonia;Intellectual disability;Cerebellar atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPOAP1 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				8	4	12
missense			17	5	7	29
nonsense	1					1
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	2	0	17	13	11

Variants in TSPOAP1

This is a list of pathogenic ClinVar variants found in the TSPOAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-58305398-C-T		Dystonia 22, adult-onset	Uncertain significance (Apr 01, 2023)
17-58305558-G-A			Likely benign (Apr 01, 2023)
17-58305843-C-T			Likely benign (Sep 01, 2022)
17-58306816-A-G			Benign (Dec 26, 2017)
17-58307604-C-T			Likely benign (Jul 11, 2018)
17-58307630-C-T		TSPOAP1-related Dystonia • not specified	Uncertain significance (Aug 09, 2021)
17-58307672-A-G		not specified	Uncertain significance (Oct 06, 2021)
17-58308572-G-A		not specified	Uncertain significance (Aug 17, 2021)
17-58308611-G-C		not specified	Uncertain significance (Aug 13, 2021)
17-58308621-G-A		not specified	Uncertain significance (Nov 09, 2021)
17-58308636-G-A			Benign (Jul 06, 2018)
17-58308656-G-A		not specified	Uncertain significance (Jun 11, 2021)
17-58308839-C-T		not specified	Uncertain significance (Sep 16, 2021)
17-58308856-A-G			Likely benign (Jul 01, 2022)
17-58308996-C-T		not specified	Uncertain significance (Oct 29, 2021)
17-58308997-T-A			Benign (Nov 26, 2019)
17-58309273-C-T			Benign (Jul 04, 2018)
17-58309361-C-T			Likely benign (Jul 11, 2018)
17-58309371-C-T		not specified	Benign (Mar 29, 2016)
17-58309372-G-A			Likely benign (Jul 19, 2018)
17-58310100-C-T			Benign (Feb 01, 2023)
17-58310741-C-A			Benign (Feb 09, 2018)
17-58310891-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-58310934-G-A			Likely benign (Jul 15, 2018)
17-58311725-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPOAP1	protein_coding	protein_coding	ENST00000343736	31	27561

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00844	0.992	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	942	1.08e+3	0.873	0.0000653	11732
Missense in Polyphen		217	289.63	0.74924		3352
Synonymous	0.464	446	459	0.972	0.0000279	3974
Loss of Function	6.56	23	90.2	0.255	0.00000519	963

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000236	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000153	0.000149
Middle Eastern	0.000218	0.000217
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Benzodiazepine Pathway, Pharmacodynamics;Metabolism of lipids;Metabolism;Pregnenolone biosynthesis;Neuronal System;Metabolism of steroid hormones;Metabolism of steroids;Glutamate Neurotransmitter Release Cycle;Dopamine Neurotransmitter Release Cycle;Acetylcholine Neurotransmitter Release Cycle;Neurotransmitter release cycle;Transmission across Chemical Synapses;Serotonin Neurotransmitter Release Cycle;Norepinephrine Neurotransmitter Release Cycle;Steroid hormones (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• rvis_EVS: 2.28
• rvis_percentile_EVS: 98.27

Haploinsufficiency Scores

• pHI: 0.237
• hipred: N
• hipred_score: 0.328
• ghis: 0.457

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tspoap1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype

Gene ontology

• Biological process: C21-steroid hormone biosynthetic process;neuromuscular synaptic transmission;biological_process;regulation of presynaptic cytosolic calcium ion concentration
• Cellular component: cytoplasm;mitochondrion;cytosol;calyx of Held;glutamatergic synapse
• Molecular function: protein binding;benzodiazepine receptor binding;voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels