ILKAP

Chr 2

ILK associated serine/threonine phosphatase

Also known as: ILKAP2, ILKAP3, PP2C-DELTA, PP2CD, PPM1O

NCBI Gene: 80895ENSG00000132323UniProt: Q9H0C8

The protein encoded by ILKAP is a serine/threonine phosphatase that regulates cell cycle progression through dephosphorylation of substrates and modulates the integrin-linked kinase (ILK) signaling pathway, including inhibition of the ILK-GSK3B axis involved in cell adhesion and growth factor signaling. This gene is highly constrained against loss-of-function variants (pLI=0.98, LOEUF=0.30), but no established Mendelian disease associations have been reported to date.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
3
Pubs (1 yr)
84
P/LP submissions
0%
P/LP missense
0.30
LOEUF· LoF intol.
LOF
Mechanism· predicted
Clinical Summary— ILKAP
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
82 unique Pathogenic / Likely Pathogenic· 38 VUS of 142 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.30LOEUF
pLI 0.981
Z-score 3.84
OE 0.10 (0.04–0.30)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.21Z-score
OE missense 0.59 (0.52–0.68)
138 obs / 232.9 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.10 (0.04–0.30)
0≤0.351.4
Missense OE0.59 (0.52–0.68)
0≤0.61.4
Synonymous OE1.02
0≤1.21.6
LoF obs/exp: 2 / 20.9Missense obs/exp: 138 / 232.9Syn Z: -0.16
DN
0.4388th %ile
GOF
0.4480th %ile
LOF
0.68top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.30

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

142 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic80
Likely Pathogenic2
VUS38
Benign1
80
Pathogenic
2
Likely Pathogenic
38
VUS
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
80
0
80
Likely Pathogenic
0
0
2
0
2
VUS
0
31
7
0
38
Likely Benign
0
0
0
0
0
Benign
0
0
0
1
1
Total031891121

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ILKAP · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 3 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients