TESC

tescalcin, the group of EF-hand domain containing

Basic information

Region (hg38): 12:117038923-117099479

Links

ENSG00000088992 ∙ NCBI:54997 ∙ OMIM:611585 ∙ HGNC:26065 ∙ Uniprot:Q96BS2 ∙ 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 TESC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TESC 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				5	4	9
missense			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	11	5	6

Variants in TESC

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

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

Position	Type	Phenotype	Significance	ClinVar
12-117039169-G-A			Benign (Sep 19, 2018)
12-117039175-G-A			Benign (Dec 31, 2019)
12-117046576-C-T			Benign (Dec 31, 2019)
12-117046583-C-T			Likely benign (Apr 30, 2018)
12-117046631-G-A			Benign (Dec 31, 2019)
12-117046646-C-T			Likely benign (Jun 28, 2018)
12-117046796-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-117046803-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-117046807-G-A			Likely benign (May 31, 2018)
12-117046812-T-C		not specified	Uncertain significance (Sep 12, 2023)
12-117046847-G-T			Benign (Dec 31, 2019)
12-117049071-G-A			Benign (May 12, 2018)
12-117049087-T-A		not specified	Uncertain significance (Mar 14, 2023)
12-117049112-C-G		not specified	Uncertain significance (May 28, 2024)
12-117049119-G-C		not specified	Uncertain significance (Jun 13, 2023)
12-117049119-G-T			Likely benign (Dec 31, 2019)
12-117049125-A-C		not specified	Uncertain significance (Jun 09, 2022)
12-117056820-G-A			Likely benign (May 09, 2018)
12-117056854-T-A		not specified	Uncertain significance (Aug 17, 2022)
12-117075323-C-T		not specified	Uncertain significance (May 27, 2022)
12-117075334-G-A		not specified	Uncertain significance (Jan 23, 2024)
12-117099266-G-A		not specified	Uncertain significance (Nov 10, 2022)
12-117099267-A-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TESC	protein_coding	protein_coding	ENST00000335209	8	60557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.108	0.886	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	95	136	0.699	0.00000879	1411
Missense in Polyphen		16	29.841	0.53618		340
Synonymous	0.456	49	53.2	0.920	0.00000394	371
Loss of Function	2.40	4	13.6	0.295	7.29e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000498	0.0000462
European (Non-Finnish)	0.0000103	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as an integral cofactor in cell pH regulation by controlling plasma membrane-type Na(+)/H(+) exchange activity. Promotes the maturation, transport, cell surface stability and exchange activity of SLC9A1/NHE1 at the plasma membrane. Promotes the induction of hematopoietic stem cell differentiation toward megakaryocytic lineage. Essential for the coupling of ERK cascade activation with the expression of ETS family genes in megakaryocytic differentiation. Also involved in granulocytic differentiation in a ERK-dependent manner. Inhibits the phosphatase activity of calcineurin. {ECO:0000269|PubMed:17717601, ECO:0000269|PubMed:18321853, ECO:0000269|PubMed:20060826}.

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.469
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.182
• hipred: Y
• hipred_score: 0.638
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.540

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tesc

Gene ontology

• Biological process: negative regulation of protein kinase activity;negative regulation of cell population proliferation;positive regulation of gene expression;protein transport;cell differentiation;positive regulation of granulocyte differentiation;positive regulation of sodium:proton antiporter activity;regulation of cell adhesion mediated by integrin;positive regulation of megakaryocyte differentiation;positive regulation of transcription, DNA-templated;protein stabilization;protein maturation;cellular response to retinoic acid;protein localization to plasma membrane
• Cellular component: ruffle;nucleus;cytoplasm;cytosol;plasma membrane;lamellipodium;ruffle membrane
• Molecular function: magnesium ion binding;protein kinase inhibitor activity;calcium ion binding;protein binding;phosphatase inhibitor activity;protein homodimerization activity