CRK
CRK proto-oncogene, adaptor protein, the group of SH2 domain containing
Basic information
Region (hg38): 17:1420689-1463162
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 CRK 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 | 4 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 3 |
Variants in CRK
This is a list of pathogenic ClinVar variants found in the CRK region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-1423517-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 17-1423533-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 17-1423553-C-T | not specified | Uncertain significance (Jan 27, 2022) | ||
| 17-1423580-C-T | not specified | Uncertain significance (Nov 24, 2024) | ||
| 17-1423621-A-C | not specified | Uncertain significance (Jan 08, 2024) | ||
| 17-1436699-A-C | not specified | Uncertain significance (Oct 25, 2024) | ||
| 17-1436708-A-G | not specified | Uncertain significance (Aug 19, 2024) | ||
| 17-1436711-G-A | not specified | Uncertain significance (Aug 05, 2024) | ||
| 17-1436716-G-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| 17-1436732-G-T | not specified | Uncertain significance (Mar 28, 2024) | ||
| 17-1436750-G-T | not specified | Uncertain significance (Mar 25, 2024) | ||
| 17-1436797-C-T | Likely benign (Jul 10, 2018) | |||
| 17-1436886-T-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 17-1437020-C-A | not specified | Uncertain significance (Jun 25, 2024) | ||
| 17-1437021-C-T | not specified | Uncertain significance (May 06, 2022) | ||
| 17-1437022-A-G | Benign (Jun 08, 2018) | |||
| 17-1437059-G-A | not specified | Uncertain significance (Jul 02, 2024) | ||
| 17-1455891-G-A | not specified | Uncertain significance (Nov 13, 2024) | ||
| 17-1455900-G-C | not specified | Uncertain significance (Aug 17, 2022) | ||
| 17-1455914-G-C | Benign (Jun 06, 2018) | |||
| 17-1455938-G-A | Benign (Dec 31, 2019) | |||
| 17-1456090-G-A | not specified | Uncertain significance (Mar 28, 2024) | ||
| 17-1456091-C-A | not specified | Uncertain significance (Jul 06, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CRK | protein_coding | protein_coding | ENST00000300574 | 3 | 42474 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.959 | 0.0406 | 124329 | 0 | 1 | 124330 | 0.00000402 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.37 | 91 | 181 | 0.504 | 0.00000962 | 1961 |
| Missense in Polyphen | 18 | 57.693 | 0.312 | 658 | ||
| Synonymous | 0.105 | 77 | 78.2 | 0.985 | 0.00000463 | 608 |
| Loss of Function | 3.27 | 1 | 14.4 | 0.0694 | 9.63e-7 | 138 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000888 | 0.00000888 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Isoform Crk-II: Regulates cell adhesion, spreading and migration. Mediates attachment-induced MAPK8 activation, membrane ruffling and cell motility in a Rac-dependent manner. Involved in phagocytosis of apoptotic cells and cell motility via its interaction with DOCK1 and DOCK4. May regulate the EFNA5-EPHA3 signaling. {ECO:0000269|PubMed:11870224, ECO:0000269|PubMed:1630456, ECO:0000269|PubMed:17515907, ECO:0000269|PubMed:19004829}.;
- Pathway
- Chronic myeloid leukemia - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Fc gamma R-mediated phagocytosis - Homo sapiens (human);Renal cell carcinoma - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);VEGF Signaling Pathway;EGF-Core;Angiogenesis overview;Integrin-mediated Cell Adhesion;Androgen Receptor Network in Prostate Cancer;B Cell Receptor Signaling Pathway;Integrated Lung Cancer Pathway;Kit receptor signaling pathway;Focal Adhesion;Signaling of Hepatocyte Growth Factor Receptor;Rac1-Pak1-p38-MMP-2 pathway;MAPK Signaling Pathway;VEGFA-VEGFR2 Signaling Pathway;Angiopoietin Like Protein 8 Regulatory Pathway;Chemokine signaling pathway;MET in type 1 papillary renal cell carcinoma;EGF-EGFR Signaling Pathway;Insulin Signaling;Regulation of Actin Cytoskeleton;Interferon type I signaling pathways;ErbB Signaling Pathway;T-Cell antigen Receptor (TCR) Signaling Pathway;Signaling by PTK6;Signal Transduction;Signaling by Interleukins;VEGFA-VEGFR2 Pathway;Cytokine Signaling in Immune system;Signaling by PDGF;Fcgamma receptor (FCGR) dependent phagocytosis;p130Cas linkage to MAPK signaling for integrins;Integrin alphaIIb beta3 signaling;HGF;TCR;ARMS-mediated activation;Innate Immune System;Immune System;KitReceptor;MET activates RAP1 and RAC1;BCR;Platelet Aggregation (Plug Formation);Platelet activation, signaling and aggregation;Prolonged ERK activation events;Signalling to ERKs;Signaling by NTRK1 (TRKA);Integrin;TGF_beta_Receptor;Signaling by NTRKs;EGFR1;Integrin signaling;CXCR4-mediated signaling events;Hemostasis;PDGF;IL2;Regulation of actin dynamics for phagocytic cup formation;VEGFR3 signaling in lymphatic endothelium;PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases;Signaling by Non-Receptor Tyrosine Kinases;Signaling events regulated by Ret tyrosine kinase;IL3;Downstream signal transduction;Signaling by VEGF;Angiopoietin receptor Tie2-mediated signaling;MET promotes cell motility;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Insulin Pathway;RAC1 signaling pathway;Nectin adhesion pathway;Neurotrophic factor-mediated Trk receptor signaling;LPA receptor mediated events;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Signaling events mediated by focal adhesion kinase;EPHB forward signaling;IGF1 pathway;JNK signaling in the CD4+ TCR pathway;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;Alpha4 beta1 integrin signaling events;PDGFR-beta signaling pathway;Signaling events mediated by PTP1B;Endothelins;PDGFR-alpha signaling pathway;E-cadherin signaling in the nascent adherens junction;EPHA forward signaling;Regulation of signaling by CBL;Interleukin-3, 5 and GM-CSF signaling
(Consensus)
Recessive Scores
- pRec
- 0.533
Intolerance Scores
- loftool
- 0.0539
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.731
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.663
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Crk
- 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); normal phenotype; 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); respiratory system phenotype; muscle phenotype; digestive/alimentary 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); growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- crk
- Affected structure
- fast muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- mononucleate
Gene ontology
- Biological process
- activation of MAPKK activity;neuron migration;response to yeast;regulation of transcription by RNA polymerase II;lipid metabolic process;regulation of cell shape;regulation of signal transduction;positive regulation of smooth muscle cell migration;dendrite development;cytokine-mediated signaling pathway;hippocampus development;cerebral cortex development;establishment of cell polarity;regulation of actin cytoskeleton organization;regulation of cell adhesion mediated by integrin;regulation of Rac protein signal transduction;helper T cell diapedesis;response to hepatocyte growth factor;reelin-mediated signaling pathway;Fc-gamma receptor signaling pathway involved in phagocytosis;response to hydrogen peroxide;regulation of GTPase activity;regulation of protein binding;negative regulation of natural killer cell mediated cytotoxicity;vascular endothelial growth factor receptor signaling pathway;ephrin receptor signaling pathway;regulation of dendrite development;cell chemotaxis;negative regulation of wound healing;response to cholecystokinin;obsolete SH2 domain-mediated complex assembly;cellular response to transforming growth factor beta stimulus;cellular response to nitric oxide;activation of GTPase activity;cerebellar neuron development;positive regulation of substrate adhesion-dependent cell spreading;cellular response to nerve growth factor stimulus;cellular response to insulin-like growth factor stimulus;cellular response to endothelin;negative regulation of cell motility;regulation of T cell migration
- Cellular component
- nucleus;cytoplasm;cytosol;plasma membrane;actin cytoskeleton;protein-containing complex;membrane raft;extracellular exosome
- Molecular function
- phosphotyrosine residue binding;SH3/SH2 adaptor activity;insulin-like growth factor receptor binding;protein binding;cytoskeletal protein binding;SH3 domain binding;SH2 domain binding;protein self-association;protein phosphorylated amino acid binding;ephrin receptor binding;scaffold protein binding;protein tyrosine kinase binding