LIMS1
protein-codingLIM zinc finger domain containing 1, the group of LIM zinc finger domain containing|LIM domain containing
Gene summary
The protein encoded by this gene is an adaptor protein which contains five LIM domains, or double zinc fingers. The protein is likely involved in integrin signaling through its LIM domain-mediated interaction with integrin-linked kinase, found in focal adhesion plaques. It is also thought to act as a bridge linking integrin-linked kinase to NCK adaptor protein 2, which is involved in growth factor receptor kinase signaling pathways. Its localization to the periphery of spreading cells also suggests that this protein may play a role in integrin-mediated cell adhesion or spreading. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~153.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LIMS1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001193483.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 42 | 42 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 44 | 0 | 0 | 44 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001180412.1 | 10 | MANE Select | |
| Ensembl | ENSP00000437912.1 | 10 | MANE Select | |
| RefSeq | NP_001180411.1 | 10 | Standard | |
| RefSeq | NP_001180413.1 | 10 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lims1 | Danio rerio | Structure: pericardium Quality: edematous abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Primary Focal Segmental Glomerulosclerosis FSGS
- Integrin-linked kinase signaling
- Regulation of cytoskeletal remodeling and cell spreading by IPP complex components
- Cell-extracellular matrix interactions
- Cell junction organization
Biological Process
- epithelial to mesenchymal transition
- cell aging
- positive regulation of gene expression
- positive regulation of cell-substrate adhesion
- tumor necrosis factor-mediated signaling pathway
Molecular Function
- protein binding
- zinc ion binding
- protein kinase binding
Cellular Component
- cytosol
- plasma membrane
- cell-cell junction
- focal adhesion
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000542845
- Coding exons
- 10
- Length
- 152846
- Individuals with no LoFs
- 114064
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11655
- Defined
- 125719
- p
- 0.0475
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.42 | 119 | 171 | 0.695 | 0.00000990 | 2538 |
| Missense (PolyPhen) | 48 | 84.707 | 0.56666 | 1180 | ||
| Synonymous | 0.359 | 60 | 63.6 | 0.943 | 0.00000399 | 655 |
| Loss of Function | 2.26 | 7 | 17.1 | 0.411 | 9.55e-7 | 257 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.029 | 0.028 | notable |
| Latino/Admixed American | 0.10 | 0.10 | notable |
| Ashkenazi Jewish | 0.014 | 0.014 | notable |
| East Asian | 0.058 | 0.057 | notable |
| Finnish | 0.037 | 0.038 | notable |
| European (Non-Finnish) | 0.037 | 0.037 | notable |
| South Asian | 0.054 | 0.053 | notable |
| Other | 0.040 | 0.040 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Adapter protein in a cytoplasmic complex linking beta- integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Involved in the regulation of cell survival, cell proliferation and cell differentiation.;
Recessive Scores
- pRec
- 0.149
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.877
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |