GeneBe

TESPA1

thymocyte expressed, positive selection associated 1

Basic information

Region (hg38): 12:54948015-54984762

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.

  • not_specified (48 variants)
  • not_provided (2 variants)

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. These statistics are base on transcript: NM_001136030.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
47
clinvar
1
clinvar
 48
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 47 3 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TESPA1protein_codingprotein_codingENST00000449076 936729
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000004690.9921249580701250280.000280
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7292452790.8770.00001463436
Missense in Polyphen6795.0270.705061185
Synonymous1.01881010.8720.00000497964
Loss of Function2.371326.10.4980.00000139283

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001030.00103
Ashkenazi Jewish0.0001990.000199
East Asian0.0001110.000110
Finnish0.00004650.0000463
European (Non-Finnish)0.0002040.000203
Middle Eastern0.0001110.000110
South Asian0.0005250.000523
Other0.0008260.000823

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerHighMediumHigh

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