TEC

tec protein tyrosine kinase, the group of SH2 domain containing|Pleckstrin homology domain containing|Tec family tyrosine kinases

Basic information

Region (hg38): 4:48135782-48269838

Links

ENSG00000135605 ∙ NCBI:7006 ∙ OMIM:600583 ∙ HGNC:11719 ∙ Uniprot:P42680 ∙ 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 TEC gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

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

Variants in TEC

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

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

Position	Type	Phenotype	Significance	ClinVar
4-48137455-T-C		not specified	Uncertain significance (Aug 16, 2022)
4-48137463-G-A		not specified	Uncertain significance (Apr 20, 2023)
4-48138706-A-C		not specified	Uncertain significance (Jan 22, 2024)
4-48138812-C-T		not specified	Uncertain significance (Dec 19, 2023)
4-48141391-G-A		not specified	Uncertain significance (Feb 03, 2022)
4-48145429-A-G		not specified	Uncertain significance (Dec 15, 2023)
4-48145529-T-C		not specified	Uncertain significance (Apr 12, 2022)
4-48149567-G-C		not specified	Uncertain significance (Dec 14, 2023)
4-48149610-T-G		not specified	Uncertain significance (Apr 18, 2023)
4-48167843-T-G		not specified	Uncertain significance (Dec 01, 2022)
4-48167900-G-C		not specified	Uncertain significance (Oct 04, 2022)
4-48167914-T-C		not specified	Uncertain significance (Jun 05, 2023)
4-48167946-G-A		not specified	Uncertain significance (Aug 15, 2023)
4-48167954-C-T			Likely pathogenic (Mar 29, 2024)
4-48176114-C-T		not specified	Uncertain significance (Sep 25, 2023)
4-48176150-T-C		not specified	Uncertain significance (Dec 13, 2022)
4-48228530-T-C		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEC	protein_coding	protein_coding	ENST00000381501	17	134082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.36e-8	1.00	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	251	333	0.753	0.0000166	4176
Missense in Polyphen		89	144.86	0.61438		1839
Synonymous	-0.715	123	113	1.09	0.00000594	1097
Loss of Function	3.14	19	40.6	0.468	0.00000212	500

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000331
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000335	0.000327
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-receptor tyrosine kinase that contributes to signaling from many receptors and participates as a signal transducer in multiple downstream pathways, including regulation of the actin cytoskeleton. Plays a redundant role to ITK in regulation of the adaptive immune response. Regulates the development, function and differentiation of conventional T-cells and nonconventional NKT-cells. Required for TCR-dependent IL2 gene induction. Phosphorylates DOK1, one CD28-specific substrate, and contributes to CD28-signaling. Mediates signals that negatively regulate IL2RA expression induced by TCR cross-linking. Plays a redundant role to BTK in BCR-signaling for B-cell development and activation, especially by phosphorylating STAP1, a BCR-signaling protein. Required in mast cells for efficient cytokine production. Involved in both growth and differentiation mechanisms of myeloid cells through activation by the granulocyte colony-stimulating factor CSF3, a critical cytokine to promoting the growth, differentiation, and functional activation of myeloid cells. Participates in platelet signaling downstream of integrin activation. Cooperates with JAK2 through reciprocal phosphorylation to mediate cytokine-driven activation of FOS transcription. GRB10, a negative modifier of the FOS activation pathway, is another substrate of TEC. TEC is involved in G protein-coupled receptor- and integrin-mediated signalings in blood platelets. Plays a role in hepatocyte proliferation and liver regeneration and is involved in HGF-induced ERK signaling pathway. TEC regulates also FGF2 unconventional secretion (endoplasmic reticulum (ER)/Golgi-independent mechanism) under various physiological conditions through phosphorylation of FGF2 'Tyr-215'. May also be involved in the regulation of osteoclast differentiation. {ECO:0000269|PubMed:10518561, ECO:0000269|PubMed:19883687, ECO:0000269|PubMed:20230531, ECO:0000269|PubMed:9753425}.
• Pathway: T cell receptor signaling pathway - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Prolactin Signaling Pathway;Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway;B Cell Receptor Signaling Pathway;JAK-STAT;Kit receptor signaling pathway;Signal Transduction;Signaling by Interleukins;Prolactin;Cytokine Signaling in Immune system;FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;TCR;Innate Immune System;Immune System;KitReceptor;BCR;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;IL3;EPO signaling pathway;Signaling by SCF-KIT;IL6;Signaling by Receptor Tyrosine Kinases;VEGF;Signaling events mediated by Stem cell factor receptor (c-Kit);Interleukin-3, 5 and GM-CSF signaling (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.280
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.88

Haploinsufficiency Scores

• pHI: 0.367
• hipred: Y
• hipred_score: 0.652
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tec
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: adaptive immune response;protein phosphorylation;integrin-mediated signaling pathway;regulation of platelet activation;peptidyl-tyrosine phosphorylation;cytokine-mediated signaling pathway;intracellular signal transduction;peptidyl-tyrosine autophosphorylation;Fc-epsilon receptor signaling pathway;tissue regeneration;positive regulation of peptidyl-tyrosine phosphorylation;T cell receptor signaling pathway;B cell receptor signaling pathway
• Cellular component: cytosol;cytoskeleton;plasma membrane
• Molecular function: non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding;phospholipid binding;metal ion binding