LIMS1

LIM zinc finger domain containing 1, the group of LIM zinc finger domain containing|LIM domain containing

Basic information

Region (hg38): 2:108533671-108687246

Links

ENSG00000169756 ∙ NCBI:3987 ∙ OMIM:602567 ∙ HGNC:6616 ∙ Uniprot:P48059 ∙ 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 LIMS1 gene.

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.

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						0
missense			31	1	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	1	1

Variants in LIMS1

This is a list of pathogenic ClinVar variants found in the LIMS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-108621404-G-A		not specified	Uncertain significance (Sep 22, 2023)
2-108621416-G-A		not specified	Uncertain significance (Jan 24, 2025)
2-108621421-G-A		not specified	Uncertain significance (Jan 04, 2024)
2-108655094-C-T		not specified	Likely benign (Jan 03, 2025)
2-108655120-G-A		not specified	Uncertain significance (Jan 17, 2025)
2-108655133-G-A		not specified	Likely benign (May 03, 2023)
2-108655147-A-G		not specified	Uncertain significance (Jul 02, 2024)
2-108655155-C-G		not specified	Uncertain significance (Oct 02, 2023)
2-108655172-A-G		not specified	Uncertain significance (May 15, 2023)
2-108655177-G-A		not specified	Uncertain significance (Jun 10, 2024)
2-108655192-A-C		not specified	Uncertain significance (Sep 27, 2022)
2-108655202-G-T		not specified	Uncertain significance (Feb 03, 2022)
2-108655204-A-G		not specified	Uncertain significance (Dec 15, 2022)
2-108655216-G-A		not specified	Uncertain significance (Mar 29, 2023)
2-108655250-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-108659633-A-G		not specified	Uncertain significance (Nov 17, 2022)
2-108659639-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-108659642-C-T		not specified	Uncertain significance (Jul 12, 2022)
2-108659661-C-T		not specified	Uncertain significance (Nov 25, 2024)
2-108659666-G-A		not specified	Uncertain significance (Jun 22, 2021)
2-108659691-G-T		not specified	Uncertain significance (Mar 04, 2025)
2-108670799-T-C		not specified	Uncertain significance (Dec 11, 2024)
2-108670806-A-T		not specified	Uncertain significance (Feb 19, 2025)
2-108670832-T-A		not specified	Uncertain significance (Oct 07, 2024)
2-108672906-G-A		not specified	Uncertain significance (Feb 28, 2025)

GnomAD

Source: gnomAD

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: dbNSFP

• 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