LIMS1
Basic information
Region (hg38): 2:108533671-108687246
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (54 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIMS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001193483.3. 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 | 0 | |||||
| missense | 34 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LIMS1 | protein_coding | protein_coding | ENST00000542845 | 10 | 152846 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00315 | 0.987 | 114064 | 0 | 11655 | 125719 | 0.0475 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.42 | 119 | 171 | 0.695 | 0.00000990 | 2538 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.130 | 0.129 |
| Ashkenazi Jewish | 0.0137 | 0.0137 |
| East Asian | 0.0580 | 0.0572 |
| Finnish | 0.0374 | 0.0379 |
| European (Non-Finnish) | 0.0366 | 0.0367 |
| Middle Eastern | 0.0580 | 0.0572 |
| South Asian | 0.0541 | 0.0531 |
| Other | 0.0404 | 0.0404 |
dbNSFP
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.;
- Pathway
- 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;Cell-Cell communication
(Consensus)
Recessive Scores
- pRec
- 0.149
Haploinsufficiency Scores
- pHI
- 0.853
- hipred
- Y
- hipred_score
- 0.594
- ghis
- 0.427
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.877
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lims1
- Phenotype
- muscle phenotype; homeostasis/metabolism phenotype; cellular 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; 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); normal phenotype; respiratory system phenotype; liver/biliary system phenotype; embryo phenotype;
Zebrafish Information Network
- Gene name
- lims1
- Affected structure
- pericardium
- Phenotype tag
- abnormal
- Phenotype quality
- edematous
Gene ontology
- 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;cell junction assembly;positive regulation of GTPase activity;establishment of protein localization;negative regulation of transcription, DNA-templated;regulation of epithelial cell proliferation;protein heterooligomerization;positive regulation of focal adhesion assembly;cellular response to transforming growth factor beta stimulus;positive regulation of substrate adhesion-dependent cell spreading;positive regulation of NIK/NF-kappaB signaling
- Cellular component
- cytosol;plasma membrane;cell-cell junction;focal adhesion;protein-containing complex;perinuclear region of cytoplasm
- Molecular function
- protein binding;zinc ion binding;protein kinase binding