PTK6
protein tyrosine kinase 6, the group of SH2 domain containing|PTK6 family tyrosine kinases
Basic information
Region (hg38): 20:63528000-63537376
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 PTK6 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 | |||||
| missense | 42 | 42 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 42 | 1 | 1 |
Variants in PTK6
This is a list of pathogenic ClinVar variants found in the PTK6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-63529543-G-C | not specified | Uncertain significance (Dec 14, 2021) | ||
| 20-63529579-C-T | not specified | Uncertain significance (Jul 26, 2022) | ||
| 20-63529580-G-A | not specified | Uncertain significance (Mar 30, 2022) | ||
| 20-63529582-A-G | not specified | Uncertain significance (Mar 14, 2023) | ||
| 20-63529598-G-T | not specified | Uncertain significance (Mar 02, 2023) | ||
| 20-63529679-G-A | not specified | Uncertain significance (Jan 19, 2024) | ||
| 20-63529688-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
| 20-63529705-G-T | not specified | Uncertain significance (Mar 25, 2024) | ||
| 20-63530141-C-T | not specified | Uncertain significance (May 09, 2023) | ||
| 20-63530147-T-C | not specified | Uncertain significance (Apr 08, 2022) | ||
| 20-63530152-G-A | not specified | Uncertain significance (Dec 18, 2023) | ||
| 20-63530162-C-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 20-63530173-G-A | not specified | Uncertain significance (Nov 30, 2021) | ||
| 20-63530180-G-T | Keratoconus | Uncertain significance (Feb 18, 2018) | ||
| 20-63530750-A-G | not specified | Uncertain significance (Sep 27, 2022) | ||
| 20-63530761-T-A | not specified | Uncertain significance (Sep 26, 2023) | ||
| 20-63530775-C-T | not specified | Uncertain significance (Jan 22, 2024) | ||
| 20-63530826-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 20-63530907-G-A | not specified | Uncertain significance (May 25, 2022) | ||
| 20-63532584-G-T | not specified | Uncertain significance (Nov 06, 2023) | ||
| 20-63532631-G-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 20-63533623-C-T | not specified | Uncertain significance (Dec 16, 2021) | ||
| 20-63533646-G-A | not specified | Uncertain significance (Mar 30, 2022) | ||
| 20-63533661-G-A | not specified | Uncertain significance (Oct 10, 2023) | ||
| 20-63533677-C-T | not specified | Uncertain significance (Dec 03, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTK6 | protein_coding | protein_coding | ENST00000217185 | 8 | 8946 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.35e-13 | 0.0498 | 125503 | 0 | 232 | 125735 | 0.000923 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.394 | 270 | 289 | 0.935 | 0.0000196 | 2904 |
| Missense in Polyphen | 84 | 101.77 | 0.8254 | 1105 | ||
| Synonymous | -0.762 | 148 | 137 | 1.08 | 0.0000101 | 900 |
| Loss of Function | 0.329 | 20 | 21.7 | 0.924 | 0.00000117 | 212 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00398 | 0.00372 |
| Ashkenazi Jewish | 0.000200 | 0.000198 |
| East Asian | 0.000994 | 0.000925 |
| Finnish | 0.000108 | 0.0000924 |
| European (Non-Finnish) | 0.000883 | 0.000836 |
| Middle Eastern | 0.000994 | 0.000925 |
| South Asian | 0.000494 | 0.000490 |
| Other | 0.00156 | 0.00147 |
dbNSFP
Source:
- Function
- FUNCTION: Non-receptor tyrosine-protein kinase implicated in the regulation of a variety of signaling pathways that control the differentiation and maintenance of normal epithelia, as well as tumor growth. Function seems to be context dependent and differ depending on cell type, as well as its intracellular localization. A number of potential nuclear and cytoplasmic substrates have been identified. These include the RNA-binding proteins: KHDRBS1/SAM68, KHDRBS2/SLM1, KHDRBS3/SLM2 and SFPQ/PSF; transcription factors: STAT3 and STAT5A/B and a variety of signaling molecules: ARHGAP35/p190RhoGAP, PXN/paxillin, BTK/ATK, STAP2/BKS. Associates also with a variety of proteins that are likely upstream of PTK6 in various signaling pathways, or for which PTK6 may play an adapter-like role. These proteins include ADAM15, EGFR, ERBB2, ERBB3 and IRS4. In normal or non-tumorigenic tissues, PTK6 promotes cellular differentiation and apoptosis. In tumors PTK6 contributes to cancer progression by sensitizing cells to mitogenic signals and enhancing proliferation, anchorage- independent survival and migration/invasion. Association with EGFR, ERBB2, ERBB3 may contribute to mammary tumor development and growth through enhancement of EGF-induced signaling via BTK/AKT and PI3 kinase. Contributes to migration and proliferation by contributing to EGF-mediated phosphorylation of ARHGAP35/p190RhoGAP, which promotes association with RASA1/p120RasGAP, inactivating RhoA while activating RAS. EGF stimulation resulted in phosphorylation of PNX/Paxillin by PTK6 and activation of RAC1 via CRK/CrKII, thereby promoting migration and invasion. PTK6 activates STAT3 and STAT5B to promote proliferation. Nuclear PTK6 may be important for regulating growth in normal epithelia, while cytoplasmic PTK6 might activate oncogenic signaling pathways.;
- Pathway
- Focal Adhesion;Signaling by PTK6;EGF-EGFR Signaling Pathway;Signaling by PTK6;Signal Transduction;ERBB2 Activates PTK6 Signaling;Cyclin D associated events in G1;G1 Phase;SCF(Skp2)-mediated degradation of p27/p21;Cyclin E associated events during G1/S transition ;PTK6 Regulates Proteins Involved in RNA Processing;PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1;PTK6 Regulates Cell Cycle;PTK6 promotes HIF1A stabilization;PTK6 Down-Regulation;PTK6 Expression;Mitotic G1-G1/S phases;PTK6 Activates STAT3;Cyclin A:Cdk2-associated events at S phase entry;S Phase;EGFR1;PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases;Signaling by Non-Receptor Tyrosine Kinases;G1/S Transition;Signaling by ERBB2;Cell Cycle;Signaling by Receptor Tyrosine Kinases;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.174
Intolerance Scores
- loftool
- 0.281
- rvis_EVS
- -1.04
- rvis_percentile_EVS
- 7.77
Haploinsufficiency Scores
- pHI
- 0.215
- hipred
- N
- hipred_score
- 0.425
- ghis
- 0.530
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.997
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptk6
- Phenotype
- digestive/alimentary phenotype;
Gene ontology
- Biological process
- protein phosphorylation;transmembrane receptor protein tyrosine kinase signaling pathway;tyrosine phosphorylation of STAT protein;negative regulation of signal transduction;positive regulation of neuron projection development;cell migration;cell differentiation;peptidyl-tyrosine autophosphorylation;ERBB2 signaling pathway;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of epidermal growth factor receptor signaling pathway;positive regulation of cell cycle;negative regulation of growth;protein autophosphorylation;intestinal epithelial cell differentiation;negative regulation of protein tyrosine kinase activity;cellular response to retinoic acid
- Cellular component
- ruffle;nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;nuclear body;extrinsic component of cytoplasmic side of plasma membrane
- Molecular function
- protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;signaling receptor binding;protein binding;ATP binding;identical protein binding