ILK
integrin linked kinase, the group of Ankyrin repeat domain containing
Basic information
Region (hg38): 11:6603708-6610874
Links
Phenotypes
GenCC
Source:
- dilated cardiomyopathy (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- Primary_familial_hypertrophic_cardiomyopathy (339 variants)
- not_specified (235 variants)
- not_provided (48 variants)
- ILK-related_disorder (12 variants)
- Cardiovascular_phenotype (2 variants)
- Cardiomyopathy (2 variants)
- Primary_dilated_cardiomyopathy (1 variants)
- Variant_of_unknown_significance (1 variants)
- ILK-related_cardiomyopathy (1 variants)
- Long_QT_syndrome (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ILK gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004517.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 125 | 128 | ||||
| missense | 216 | 12 | 229 | |||
| nonsense | 5 | |||||
| start loss | 0 | |||||
| frameshift | 8 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 0 | 0 | 234 | 137 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ILK | protein_coding | protein_coding | ENST00000396751 | 12 | 7142 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000379 | 0.998 | 125689 | 0 | 59 | 125748 | 0.000235 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.517 | 235 | 258 | 0.909 | 0.0000161 | 3004 |
| Missense in Polyphen | 74 | 91.161 | 0.81175 | 1137 | ||
| Synonymous | -1.55 | 108 | 89.4 | 1.21 | 0.00000479 | 856 |
| Loss of Function | 2.71 | 12 | 27.2 | 0.440 | 0.00000194 | 262 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000518 | 0.000514 |
| Ashkenazi Jewish | 0.000198 | 0.000198 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.000407 | 0.000370 |
| European (Non-Finnish) | 0.000266 | 0.000264 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000166 | 0.000163 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor-proximal protein kinase regulating integrin- mediated signal transduction (PubMed:8538749, PubMed:9736715). May act as a mediator of inside-out integrin signaling. Focal adhesion protein part of the complex ILK-PINCH. This complex is considered to be one of the convergence points of integrin- and growth factor-signaling pathway. Could be implicated in mediating cell architecture, adhesion to integrin substrates and anchorage- dependent growth in epithelial cells. Phosphorylates beta-1 and beta-3 integrin subunit on serine and threonine residues, but also AKT1 and GSK3B (PubMed:8538749, PubMed:9736715). {ECO:0000269|PubMed:8538749, ECO:0000269|PubMed:9736715, ECO:0000303|PubMed:10712922}.;
- Pathway
- Focal adhesion - Homo sapiens (human);Axon guidance - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Integrin-mediated Cell Adhesion;Primary Focal Segmental Glomerulosclerosis FSGS;Focal Adhesion;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;PPAR signaling pathway;Eukaryotic Transcription Initiation;Endometrial cancer;pten dependent cell cycle arrest and apoptosis;Wnt;Integrin-linked kinase signaling;Localization of the PINCH-ILK-PARVIN complex to focal adhesions;Cell-extracellular matrix interactions;Cell junction organization;Cell-Cell communication;Osteopontin-mediated events;Integrins in angiogenesis
(Consensus)
Recessive Scores
- pRec
- 0.599
Intolerance Scores
- loftool
- 0.195
- rvis_EVS
- -0.69
- rvis_percentile_EVS
- 14.97
Haploinsufficiency Scores
- pHI
- 0.641
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.982
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ilk
- Phenotype
- digestive/alimentary phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; pigmentation 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); 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); normal phenotype; 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); growth/size/body region phenotype; craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- ilk
- Affected structure
- cardiac muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- shape
Gene ontology
- Biological process
- MAPK cascade;branching involved in ureteric bud morphogenesis;positive regulation of protein phosphorylation;positive regulation of cell-matrix adhesion;outflow tract morphogenesis;protein phosphorylation;negative regulation of protein kinase activity;cell cycle arrest;cell-matrix adhesion;integrin-mediated signaling pathway;cell aging;cell population proliferation;positive regulation of cell population proliferation;positive regulation of signal transduction;negative regulation of cardiac muscle cell apoptotic process;fibroblast migration;negative regulation of smooth muscle cell migration;peptidyl-serine phosphorylation;nerve development;myelination in peripheral nervous system;positive regulation of cell migration;positive regulation of BMP signaling pathway;myelin assembly;regulation of actin cytoskeleton organization;tumor necrosis factor-mediated signaling pathway;cell junction assembly;substrate adhesion-dependent cell spreading;positive regulation of phosphorylation;positive regulation of MAP kinase activity;protein kinase B signaling;negative regulation of neuron apoptotic process;establishment or maintenance of epithelial cell apical/basal polarity;positive regulation of myoblast differentiation;positive regulation of osteoblast differentiation;positive regulation of axon extension;positive regulation of transcription, DNA-templated;negative regulation of smooth muscle cell proliferation;neuron projection morphogenesis;positive regulation of dendrite morphogenesis;protein heterooligomerization;positive regulation of protein kinase B signaling;platelet aggregation;positive regulation of canonical Wnt signaling pathway;supramolecular fiber organization;positive regulation of NIK/NF-kappaB signaling;negative regulation of neural precursor cell proliferation
- Cellular component
- stress fiber;nucleoplasm;cytosol;plasma membrane;cell-cell junction;focal adhesion;membrane;sarcomere;lamellipodium;cell junction;protein-containing complex;neuronal cell body;costamere;terminal bouton;dendritic shaft
- Molecular function
- protein serine/threonine kinase activity;integrin binding;protein binding;ATP binding;SH3 domain binding;protein kinase binding