ILK

integrin linked kinase, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 11:6603708-6610874

Links

ENSG00000166333 ∙ NCBI:3611 ∙ OMIM:602366 ∙ HGNC:6040 ∙ Uniprot:Q13418 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dilated cardiomyopathy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ILK gene.

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.

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	93	1	96
missense			169	5		174
nonsense			4			4
start loss						0
frameshift			3			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)			2			2
splice region			10	12		22
non coding			3	61	9	73
Total	0	0	184	159	10

Variants in ILK

This is a list of pathogenic ClinVar variants found in the ILK region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-6603786-G-T			Benign (Jun 14, 2018)
11-6603802-G-T		not specified	Likely benign (Feb 22, 2016)
11-6603806-C-T		not specified	Likely benign (Apr 01, 2016)
11-6603807-T-C		not specified	Benign (May 29, 2014)
11-6603810-A-G		not specified	Likely benign (Nov 09, 2015)
11-6603972-G-C			Likely benign (Jul 11, 2018)
11-6604085-A-G			Likely benign (Jul 11, 2018)
11-6604141-A-G			Likely benign (Jun 16, 2018)
11-6604256-G-A		not specified	Likely benign (May 08, 2017)
11-6604278-G-C		Primary familial hypertrophic cardiomyopathy	Uncertain significance (Nov 25, 2019)
11-6604283-T-A		not specified • Primary familial hypertrophic cardiomyopathy	Likely benign (Feb 12, 2022)
11-6604286-C-T		Primary familial hypertrophic cardiomyopathy	Likely benign (May 15, 2023)
11-6604292-G-A		not specified	Likely benign (Jan 13, 2023)
11-6604306-A-G		Primary familial hypertrophic cardiomyopathy	Uncertain significance (Feb 18, 2020)
11-6604307-C-T		Primary familial hypertrophic cardiomyopathy • ILK-related disorder • not specified	Benign/Likely benign (Dec 14, 2022)
11-6604317-G-T		not specified	Uncertain significance (Jan 17, 2024)
11-6604323-C-T		Primary familial hypertrophic cardiomyopathy • not specified	Likely benign (Jun 27, 2023)
11-6604334-C-T		Primary familial hypertrophic cardiomyopathy • not specified	Likely benign (Apr 04, 2022)
11-6604336-A-G		not specified • Primary familial hypertrophic cardiomyopathy • Cardiomyopathy • ILK-related disorder	Likely benign (Jan 22, 2024)
11-6604338-A-T		not specified	Uncertain significance (Jul 19, 2023)
11-6604340-G-C		Primary familial hypertrophic cardiomyopathy	Likely benign (Dec 19, 2019)
11-6604343-G-A		not specified	Likely benign (Aug 12, 2019)
11-6604349-C-A		not specified	Uncertain significance (Apr 01, 2023)
11-6604350-C-A		Primary familial hypertrophic cardiomyopathy	Uncertain significance (Nov 13, 2021)
11-6604354-A-G		Primary familial hypertrophic cardiomyopathy	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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