TESPA1

thymocyte expressed, positive selection associated 1

Basic information

Region (hg38): 12:54948014-54984762

Previous symbols: [ "KIAA0748" ]

Links

ENSG00000135426 ∙ NCBI:9840 ∙ OMIM:615664 ∙ HGNC:29109 ∙ Uniprot:A2RU30 ∙ 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 TESPA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TESPA1 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				2		2
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	0

Variants in TESPA1

This is a list of pathogenic ClinVar variants found in the TESPA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54961219-T-C		not specified	Uncertain significance (Dec 06, 2021)
12-54961241-C-T			Likely benign (Oct 01, 2021)
12-54961248-T-C		not specified	Uncertain significance (Aug 10, 2023)
12-54962479-C-T			Likely benign (Jun 01, 2022)
12-54962544-C-G		not specified	Uncertain significance (Apr 06, 2022)
12-54962602-C-A		not specified	Uncertain significance (Dec 08, 2023)
12-54962640-T-C		not specified	Uncertain significance (Mar 19, 2024)
12-54962744-T-A		not specified	Uncertain significance (Jul 05, 2022)
12-54962747-G-A		not specified	Uncertain significance (May 04, 2023)
12-54962859-G-A		not specified	Uncertain significance (Apr 08, 2024)
12-54962876-T-A		not specified	Uncertain significance (Aug 14, 2023)
12-54962877-G-C		not specified	Uncertain significance (Oct 26, 2022)
12-54962932-T-G		not specified	Uncertain significance (Jul 09, 2021)
12-54962962-C-G		not specified	Uncertain significance (Jul 25, 2023)
12-54963005-T-C		not specified	Uncertain significance (Dec 27, 2023)
12-54963063-G-T		not specified	Uncertain significance (Aug 10, 2021)
12-54963083-C-T		not specified	Uncertain significance (Aug 30, 2021)
12-54963154-C-A		not specified	Uncertain significance (Dec 26, 2023)
12-54963158-T-A		not specified	Uncertain significance (Sep 16, 2021)
12-54963182-G-A		not specified	Uncertain significance (Oct 05, 2023)
12-54963780-C-T		not specified	Likely benign (Dec 22, 2023)
12-54963850-C-A		not specified	Uncertain significance (Apr 09, 2024)
12-54974463-C-A		not specified	Uncertain significance (Jul 06, 2021)
12-54974471-T-A		not specified	Uncertain significance (Sep 26, 2023)
12-54974494-G-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TESPA1	protein_coding	protein_coding	ENST00000449076	9	36729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000469	0.992	124958	0	70	125028	0.000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.729	245	279	0.877	0.0000146	3436
Missense in Polyphen		67	95.027	0.70506		1185
Synonymous	1.01	88	101	0.872	0.00000497	964
Loss of Function	2.37	13	26.1	0.498	0.00000139	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00103
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000111	0.000110
Finnish	0.0000465	0.0000463
European (Non-Finnish)	0.000204	0.000203
Middle Eastern	0.000111	0.000110
South Asian	0.000525	0.000523
Other	0.000826	0.000823

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the development and maturation of T-cells, its function being essential for the late stages of thymocyte development (By similarity). Plays a role in T-cell antigen receptor (TCR)-mediated activation of the ERK and NFAT signaling pathways, possibly by serving as a scaffolding protein that promotes the assembly of the LAT signalosome in thymocytes. May play a role in the regulation of inositol 1,4,5-trisphosphate receptor-mediated Ca(2+) release and mitochondrial Ca(2+) uptake via the mitochondria-associated endoplasmic reticulum membrane (MAM) compartment. {ECO:0000250, ECO:0000269|PubMed:22561606}.

Intolerance Scores

• rvis_EVS: 1.49
• rvis_percentile_EVS: 95.35

Haploinsufficiency Scores

• pHI: 0.205
• hipred: N
• hipred_score: 0.146
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tespa1
• Phenotype: immune system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: COP9 signalosome assembly;positive regulation of T cell differentiation in thymus;positive regulation of T cell receptor signaling pathway
• Cellular component: cytoplasm;endoplasmic reticulum membrane;COP9 signalosome
• Molecular function: signaling receptor binding