CRKL
CRK like proto-oncogene, adaptor protein, the group of SH2 domain containing
Basic information
Region (hg38): 22:20917407-20953747
Links
Phenotypes
GenCC
Source:
- congenital heart disease (No Known Disease Relationship), mode of inheritance: Unknown
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 CRKL 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 | 10 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 11 | 9 | 3 |
Variants in CRKL
This is a list of pathogenic ClinVar variants found in the CRKL region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-20917961-G-A | Likely benign (Dec 05, 2023) | |||
| 22-20917970-C-T | CRKL-related disorder | Benign (Dec 27, 2023) | ||
| 22-20917973-C-T | CRKL-related disorder | Likely benign (Mar 20, 2019) | ||
| 22-20918010-AC-A | Uncertain significance (Nov 01, 2023) | |||
| 22-20918024-C-T | Likely benign (Jul 30, 2022) | |||
| 22-20918037-A-G | not specified | Uncertain significance (Nov 09, 2023) | ||
| 22-20918060-C-T | Likely benign (May 20, 2022) | |||
| 22-20918075-CTA-C | Uncertain significance (Jul 08, 2022) | |||
| 22-20918183-C-T | Likely benign (Sep 08, 2022) | |||
| 22-20918223-A-G | Uncertain significance (Oct 06, 2023) | |||
| 22-20918247-T-C | Uncertain significance (Aug 01, 2023) | |||
| 22-20918251-C-T | Uncertain significance (Nov 12, 2022) | |||
| 22-20933804-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 22-20933820-T-G | CRKL-related disorder | Uncertain significance (Jun 26, 2024) | ||
| 22-20933973-G-A | not specified | Uncertain significance (Aug 02, 2023) | ||
| 22-20933999-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 22-20934001-C-T | Likely benign (Jul 06, 2018) | |||
| 22-20934088-C-T | CRKL-related disorder | Likely benign (Feb 21, 2019) | ||
| 22-20934127-C-T | Likely benign (Apr 25, 2023) | |||
| 22-20934128-G-A | CRKL-related disorder | Benign (Jan 12, 2024) | ||
| 22-20934144-C-T | Uncertain significance (Oct 04, 2022) | |||
| 22-20934166-A-T | Likely benign (Dec 31, 2019) | |||
| 22-20949691-T-C | Benign (Jul 16, 2023) | |||
| 22-20949721-T-C | Uncertain significance (Jun 17, 2021) | |||
| 22-20949722-C-T | Likely benign (Jul 20, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CRKL | protein_coding | protein_coding | ENST00000354336 | 3 | 36324 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.446 | 0.548 | 125740 | 0 | 4 | 125744 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.94 | 105 | 178 | 0.591 | 0.00000943 | 1973 |
| Missense in Polyphen | 23 | 68.177 | 0.33736 | 767 | ||
| Synonymous | -2.03 | 98 | 75.6 | 1.30 | 0.00000447 | 633 |
| Loss of Function | 2.31 | 2 | 9.82 | 0.204 | 4.23e-7 | 118 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000267 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May mediate the transduction of intracellular signals.;
- 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);Androgen Receptor Network in Prostate Cancer;B Cell Receptor Signaling Pathway;IL-3 Signaling Pathway;Kit receptor signaling pathway;Focal Adhesion;Signaling of Hepatocyte Growth Factor Receptor;MAPK Signaling Pathway;Chemokine signaling pathway;MET in type 1 papillary renal cell carcinoma;EGF-EGFR Signaling Pathway;IL-2 Signaling Pathway;Interferon type I signaling pathways;T-Cell antigen Receptor (TCR) Signaling Pathway;Signal Transduction;Signaling by Interleukins;inhibition of cellular proliferation by gleevec;links between pyk2 and map kinases;angiotensin ii mediated activation of jnk pathway via pyk2 dependent signaling;integrin signaling pathway;il-2 receptor beta chain in t cell activation;Cytokine Signaling in Immune system;GPCR Adenosine A2A receptor;Signaling by PDGF;HGF;TCR;Immune System;KitReceptor;MET activates RAP1 and RAC1;BCR;GPCR signaling-G alpha s PKA and ERK;Frs2-mediated activation;Prolonged ERK activation events;Signalling to ERKs;Signaling by NTRK1 (TRKA);Signaling by NTRKs;EGFR1;IL2;IL3;Downstream signal transduction;IFN-gamma pathway;EPO signaling pathway;IL5;MET promotes cell motility;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Neurotrophic factor-mediated Trk receptor signaling;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Reelin signaling pathway;IGF1 pathway;Signaling events mediated by Stem cell factor receptor (c-Kit);JNK signaling in the CD4+ TCR pathway;PDGFR-alpha signaling pathway;EPHA forward signaling;Regulation of signaling by CBL;Interleukin-3, 5 and GM-CSF signaling
(Consensus)
Recessive Scores
- pRec
- 0.440
Intolerance Scores
- loftool
- 0.0613
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.953
- hipred
- Y
- hipred_score
- 0.849
- ghis
- 0.677
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- 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
- Crkl
- Phenotype
- embryo phenotype; liver/biliary system 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); hematopoietic system 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); neoplasm; limbs/digits/tail 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); hearing/vestibular/ear phenotype; vision/eye phenotype; immune system phenotype; skeleton 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; endocrine/exocrine gland phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- crkl
- Affected structure
- fast muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- mononucleate
Gene ontology
- Biological process
- activation of MAPKK activity;activation of MAPK activity;regulation of cell growth;blood vessel development;urogenital system development;neuron migration;B cell apoptotic process;negative regulation of protein phosphorylation;positive regulation of protein phosphorylation;outflow tract morphogenesis;lipid metabolic process;JNK cascade;Ras protein signal transduction;spermatogenesis;single fertilization;synapse assembly;positive regulation of cell population proliferation;fibroblast growth factor receptor signaling pathway;male gonad development;anterior/posterior pattern specification;negative regulation of gene expression;dendrite development;cytokine-mediated signaling pathway;hippocampus development;cerebral cortex development;establishment of cell polarity;regulation of cell adhesion mediated by integrin;intracellular signal transduction;helper T cell diapedesis;reelin-mediated signaling pathway;positive regulation of Ras protein signal transduction;retinoic acid receptor signaling pathway;thymus development;regulation of dendrite development;T cell receptor signaling pathway;parathyroid gland development;cell chemotaxis;pharynx development;positive regulation of ERK1 and ERK2 cascade;cellular response to transforming growth factor beta stimulus;endothelin receptor signaling pathway;activation of GTPase activity;acetylcholine receptor signaling pathway;cerebellar neuron development;cellular response to interleukin-7;positive regulation of substrate adhesion-dependent cell spreading;positive regulation of glial cell migration;regulation of skeletal muscle acetylcholine-gated channel clustering;cranial skeletal system development;regulation of T cell migration
- Cellular component
- nucleoplasm;cytosol;neuromuscular junction;protein-containing complex;extrinsic component of postsynaptic membrane
- Molecular function
- phosphotyrosine residue binding;RNA binding;SH3/SH2 adaptor activity;protein binding;identical protein binding;cadherin binding