ILKAP

ILK associated serine/threonine phosphatase, the group of Protein phosphatases, Mg2+/Mn2+ dependent

Basic information

Region (hg38): 2:238170402-238203708

Links

ENSG00000132323 ∙ NCBI:80895 ∙ OMIM:618909 ∙ HGNC:15566 ∙ Uniprot:Q9H0C8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ILKAP 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					1	1
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	1

Variants in ILKAP

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

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

Position	Type	Phenotype	Significance	ClinVar
2-238170549-C-T		not specified	Uncertain significance (Nov 03, 2022)
2-238170625-C-T		not specified	Uncertain significance (Nov 15, 2021)
2-238170635-G-A			Benign (Jun 26, 2018)
2-238170637-C-T		not specified	Uncertain significance (Apr 07, 2023)
2-238170660-G-T		not specified	Uncertain significance (May 23, 2023)
2-238170668-C-A		not specified	Uncertain significance (May 09, 2023)
2-238173540-T-C		not specified	Uncertain significance (Nov 03, 2023)
2-238173566-G-C		not specified	Uncertain significance (Oct 25, 2023)
2-238173599-C-G		not specified	Uncertain significance (Aug 02, 2022)
2-238173634-C-T		not specified	Uncertain significance (Mar 15, 2024)
2-238182156-G-T		not specified	Uncertain significance (Oct 05, 2023)
2-238182159-T-A		not specified	Uncertain significance (Aug 21, 2023)
2-238188251-G-A		not specified	Uncertain significance (May 08, 2023)
2-238189922-C-T		not specified	Uncertain significance (Apr 18, 2023)
2-238189925-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-238189926-T-A		not specified	Uncertain significance (Dec 14, 2023)
2-238194281-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-238194296-G-C		not specified	Uncertain significance (Nov 24, 2024)
2-238194820-T-C		not specified	Uncertain significance (Mar 13, 2023)
2-238194858-T-C		not specified	Uncertain significance (Apr 08, 2022)
2-238203516-G-A		not specified	Uncertain significance (Nov 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ILKAP	protein_coding	protein_coding	ENST00000254654	12	33329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.981	0.0188	125733	0	4	125737	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	138	233	0.593	0.0000142	2550
Missense in Polyphen		35	91.659	0.38185		895
Synonymous	-0.155	94	92.1	1.02	0.00000622	757
Loss of Function	3.84	2	20.9	0.0955	9.48e-7	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase that may play a role in regulation of cell cycle progression via dephosphorylation of its substrates whose appropriate phosphorylation states might be crucial for cell proliferation. Selectively associates with integrin linked kinase (ILK), to modulate cell adhesion and growth factor signaling. Inhibits the ILK-GSK3B signaling axis and may play an important role in inhibiting oncogenic transformation. {ECO:0000269|PubMed:14990992}.
• Pathway: Integrin-linked kinase signaling (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.167
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.994
• hipred: Y
• hipred_score: 0.738
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.717

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ilkap
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein dephosphorylation
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;protein binding;metal ion binding