TEC
tec protein tyrosine kinase, the group of SH2 domain containing|Pleckstrin homology domain containing|Tec family tyrosine kinases
Basic information
Region (hg38): 4:48135783-48269838
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 1 | 16 | 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) | ||
| 4-48138768-G-A | not specified | Uncertain significance (May 06, 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) | ||
| 4-48145492-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 4-48145529-T-C | not specified | Uncertain significance (Jun 16, 2024) | ||
| 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) | ||
| 4-48228500-T-C | not specified | Uncertain significance (Apr 19, 2024) | ||
| 4-48228530-T-C | not specified | Uncertain significance (Feb 16, 2023) |
GnomAD
Source:
| 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:
- 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