PTK2
protein tyrosine kinase 2, the group of PTK2 family tyrosine kinases|Protein phosphatase 1 regulatory subunits|MicroRNA protein coding host genes|FERM domain containing
Basic information
Region (hg38): 8:140657900-141002216
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 PTK2 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 | 17 | |||||
| missense | 31 | 33 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 32 | 11 | 10 |
Variants in PTK2
This is a list of pathogenic ClinVar variants found in the PTK2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-140658761-A-T | Benign (Feb 18, 2020) | |||
| 8-140659606-A-G | not specified | Uncertain significance (May 31, 2023) | ||
| 8-140659629-T-C | not specified | Likely benign (Jun 06, 2023) | ||
| 8-140664945-G-A | not specified | Uncertain significance (Apr 06, 2024) | ||
| 8-140664946-G-C | not specified | Uncertain significance (Oct 05, 2021) | ||
| 8-140668299-G-A | Benign (Dec 31, 2019) | |||
| 8-140668309-A-G | not specified | Uncertain significance (May 24, 2024) | ||
| 8-140668316-T-C | not specified | Uncertain significance (Aug 10, 2021) | ||
| 8-140668343-G-A | Likely benign (Jul 16, 2018) | |||
| 8-140668348-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 8-140668359-G-A | Benign (Sep 01, 2022) | |||
| 8-140668370-C-A | not specified | Uncertain significance (Feb 21, 2024) | ||
| 8-140668380-G-C | not specified | Uncertain significance (May 03, 2023) | ||
| 8-140668387-T-C | not specified | Uncertain significance (Aug 10, 2021) | ||
| 8-140674360-C-T | not specified | Uncertain significance (Aug 16, 2021) | ||
| 8-140674396-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
| 8-140700903-C-T | Benign/Likely benign (Sep 01, 2022) | |||
| 8-140700919-C-T | not specified | Uncertain significance (Apr 04, 2024) | ||
| 8-140700950-G-A | 11 conditions | Uncertain significance (Mar 24, 2023) | ||
| 8-140701005-G-T | not specified | Uncertain significance (May 06, 2024) | ||
| 8-140701018-G-C | not specified | Uncertain significance (Sep 27, 2022) | ||
| 8-140702572-C-T | not specified | Uncertain significance (May 17, 2023) | ||
| 8-140702593-C-T | Likely benign (Jul 18, 2018) | |||
| 8-140702595-A-G | not specified | Uncertain significance (May 05, 2023) | ||
| 8-140702657-G-C | not specified | Uncertain significance (Aug 16, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTK2 | protein_coding | protein_coding | ENST00000340930 | 31 | 344317 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000125 | 125734 | 0 | 14 | 125748 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.44 | 358 | 594 | 0.603 | 0.0000316 | 6992 |
| Missense in Polyphen | 95 | 237.52 | 0.39996 | 2701 | ||
| Synonymous | -0.373 | 218 | 211 | 1.03 | 0.0000118 | 1959 |
| Loss of Function | 6.62 | 10 | 69.7 | 0.144 | 0.00000376 | 804 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.0000939 | 0.0000924 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Non-receptor protein-tyrosine kinase that plays an essential role in regulating cell migration, adhesion, spreading, reorganization of the actin cytoskeleton, formation and disassembly of focal adhesions and cell protrusions, cell cycle progression, cell proliferation and apoptosis. Required for early embryonic development and placenta development. Required for embryonic angiogenesis, normal cardiomyocyte migration and proliferation, and normal heart development. Regulates axon growth and neuronal cell migration, axon branching and synapse formation; required for normal development of the nervous system. Plays a role in osteogenesis and differentiation of osteoblasts. Functions in integrin signal transduction, but also in signaling downstream of numerous growth factor receptors, G-protein coupled receptors (GPCR), EPHA2, netrin receptors and LDL receptors. Forms multisubunit signaling complexes with SRC and SRC family members upon activation; this leads to the phosphorylation of additional tyrosine residues, creating binding sites for scaffold proteins, effectors and substrates. Regulates numerous signaling pathways. Promotes activation of phosphatidylinositol 3-kinase and the AKT1 signaling cascade. Promotes activation of MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling cascade. Promotes localized and transient activation of guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs), and thereby modulates the activity of Rho family GTPases. Signaling via CAS family members mediates activation of RAC1. Recruits the ubiquitin ligase MDM2 to P53/TP53 in the nucleus, and thereby regulates P53/TP53 activity, P53/TP53 ubiquitination and proteasomal degradation. Phosphorylates SRC; this increases SRC kinase activity. Phosphorylates ACTN1, ARHGEF7, GRB7, RET and WASL. Promotes phosphorylation of PXN and STAT1; most likely PXN and STAT1 are phosphorylated by a SRC family kinase that is recruited to autophosphorylated PTK2/FAK1, rather than by PTK2/FAK1 itself. Promotes phosphorylation of BCAR1; GIT2 and SHC1; this requires both SRC and PTK2/FAK1. Promotes phosphorylation of BMX and PIK3R1. Isoform 6 (FRNK) does not contain a kinase domain and inhibits PTK2/FAK1 phosphorylation and signaling. Its enhanced expression can attenuate the nuclear accumulation of LPXN and limit its ability to enhance serum response factor (SRF)-dependent gene transcription. {ECO:0000269|PubMed:10655584, ECO:0000269|PubMed:11331870, ECO:0000269|PubMed:11980671, ECO:0000269|PubMed:15166238, ECO:0000269|PubMed:15561106, ECO:0000269|PubMed:15895076, ECO:0000269|PubMed:16919435, ECO:0000269|PubMed:16927379, ECO:0000269|PubMed:17395594, ECO:0000269|PubMed:17431114, ECO:0000269|PubMed:17968709, ECO:0000269|PubMed:18006843, ECO:0000269|PubMed:18206965, ECO:0000269|PubMed:18256281, ECO:0000269|PubMed:18292575, ECO:0000269|PubMed:18497331, ECO:0000269|PubMed:18677107, ECO:0000269|PubMed:19138410, ECO:0000269|PubMed:19147981, ECO:0000269|PubMed:19224453, ECO:0000269|PubMed:20332118, ECO:0000269|PubMed:20495381, ECO:0000269|PubMed:21454698}.;
- Disease
- DISEASE: Note=Aberrant PTK2/FAK1 expression may play a role in cancer cell proliferation, migration and invasion, in tumor formation and metastasis. PTK2/FAK1 overexpression is seen in many types of cancer.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Focal adhesion - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Androgen receptor signaling pathway;RANKL-RANK (Receptor activator of NFKB (ligand)) Signaling Pathway;Integrin-mediated Cell Adhesion;Leptin signaling pathway;Prolactin Signaling Pathway;Corticotropin-releasing hormone signaling pathway;Alpha 6 Beta 4 signaling pathway;Primary Focal Segmental Glomerulosclerosis FSGS;JAK-STAT;Apoptosis-related network due to altered Notch3 in ovarian cancer;Focal Adhesion;Signaling of Hepatocyte Growth Factor Receptor;Overview of nanoparticle effects;MFAP5-mediated ovarian cancer cell motility and invasiveness;Rac1-Pak1-p38-MMP-2 pathway;TGF-beta Signaling Pathway;Association Between Physico-Chemical Features and Toxicity Associated Pathways;VEGFA-VEGFR2 Signaling Pathway;Chemokine signaling pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Prion disease pathway;PI3K-Akt Signaling Pathway;MET in type 1 papillary renal cell carcinoma;EGF-EGFR Signaling Pathway;Regulation of Actin Cytoskeleton;ErbB Signaling Pathway;Developmental Biology;Signal Transduction;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;ucalpain and friends in cell spread;integrin signaling pathway;phospholipids as signalling intermediaries;ccr3 signaling in eosinophils;pten dependent cell cycle arrest and apoptosis;vegf hypoxia and angiogenesis;hiv-1 nef: negative effector of fas and tnf;mcalpain and friends in cell motility;VEGFA-VEGFR2 Pathway;Prolactin;Alpha6Beta4Integrin;Fcgamma receptor (FCGR) dependent phagocytosis;GRB2:SOS provides linkage to MAPK signaling for Integrins ;p130Cas linkage to MAPK signaling for integrins;Integrin alphaIIb beta3 signaling;EPH-Ephrin signaling;TCR;Apoptotic cleavage of cellular proteins;Innate Immune System;Immune System;EPHB-mediated forward signaling;Apoptotic execution phase;Apoptosis;RHO GTPases Activate WASPs and WAVEs;Programmed Cell Death;Fibroblast growth factor-1;BCR;AndrogenReceptor;CRH;Platelet Aggregation (Plug Formation);cell to cell adhesion signaling;Platelet activation, signaling and aggregation;IL-7 signaling;RHO GTPase Effectors;Signaling by Rho GTPases;DCC mediated attractive signaling;Integrin;Netrin mediated repulsion signals;TGF_beta_Receptor;role of nicotinic acetylcholine receptors in the regulation of apoptosis;EGFR1;agrin in postsynaptic differentiation;Integrin signaling;CXCR4-mediated signaling events;Hemostasis;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;JAK STAT pathway and regulation;Regulation of actin dynamics for phagocytic cup formation;NCAM signaling for neurite out-growth;EPO signaling;Netrin-1 signaling;Signaling events regulated by Ret tyrosine kinase;Gastrin;Signaling by VEGF;Angiopoietin receptor Tie2-mediated signaling;IL4;Axon guidance;Leptin;TNFalpha;MET activates PTK2 signaling;MET promotes cell motility;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Signal regulatory protein family interactions;VEGF;Cell-Cell communication;RANKL;Caspase Cascade in Apoptosis;a4b7 Integrin signaling;Nectin adhesion pathway;LPA receptor mediated events;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Fc-epsilon receptor I signaling in mast cells;Internalization of ErbB1;Netrin-mediated signaling events;Signaling events mediated by focal adhesion kinase;EPHB forward signaling;IGF1 pathway;Nongenotropic Androgen signaling;Alpha4 beta1 integrin signaling events;EPHA2 forward signaling;Syndecan-4-mediated signaling events;Signaling events mediated by VEGFR1 and VEGFR2;Integrins in angiogenesis
(Consensus)
Intolerance Scores
- loftool
- 0.286
- rvis_EVS
- -1.51
- rvis_percentile_EVS
- 3.54
Haploinsufficiency Scores
- pHI
- 0.869
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.589
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.965
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptk2
- Phenotype
- respiratory system phenotype; liver/biliary system phenotype; embryo phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype;
Zebrafish Information Network
- Gene name
- ptk2ab
- Affected structure
- lens
- Phenotype tag
- abnormal
- Phenotype quality
- separated from
Gene ontology
- Biological process
- MAPK cascade;microtubule cytoskeleton organization;angiogenesis;vasculogenesis;neuron migration;placenta development;regulation of protein phosphorylation;positive regulation of protein phosphorylation;heart morphogenesis;nuclear migration;signal complex assembly;epidermal growth factor receptor signaling pathway;transforming growth factor beta receptor signaling pathway;integrin-mediated signaling pathway;axon guidance;positive regulation of cell population proliferation;regulation of cell shape;negative regulation of autophagy;regulation of endothelial cell migration;positive regulation of cardiac muscle hypertrophy;regulation of epithelial cell migration;positive regulation of phosphatidylinositol 3-kinase signaling;peptidyl-tyrosine phosphorylation;central nervous system neuron axonogenesis;negative regulation of cell-cell adhesion;establishment of cell polarity;cell differentiation;regulation of cell adhesion;extracellular matrix organization;positive regulation of cell migration;regulation of cell adhesion mediated by integrin;netrin-activated signaling pathway;peptidyl-tyrosine autophosphorylation;Fc-gamma receptor signaling pathway involved in phagocytosis;regulation of cell population proliferation;negative regulation of apoptotic process;regulation of GTPase activity;endothelial cell migration;positive regulation of phosphatidylinositol 3-kinase activity;regulation of osteoblast differentiation;positive regulation of protein kinase activity;negative regulation of organ growth;protein autophosphorylation;vascular endothelial growth factor receptor signaling pathway;ephrin receptor signaling pathway;cell motility;negative regulation of axonogenesis;regulation of cytoskeleton organization;regulation of focal adhesion assembly;positive regulation of protein kinase B signaling;negative regulation of synapse assembly;growth hormone receptor signaling pathway;regulation of substrate adhesion-dependent cell spreading;positive regulation of ubiquitin-dependent protein catabolic process;negative regulation of anoikis
- Cellular component
- stress fiber;nucleus;cytoplasm;microtubule organizing center;cytosol;cytoskeleton;plasma membrane;focal adhesion;cell cortex;apical plasma membrane;lamellipodium;dendritic spine
- Molecular function
- actin binding;protein kinase activity;protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;Ras guanyl-nucleotide exchange factor activity;protein binding;ATP binding;JUN kinase binding;protein kinase binding;protein phosphatase binding;SH2 domain binding