Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	55679
Gene name	LIM zinc finger domain containing 2
Gene symbol	LIMS2
Synonyms (NCBI Gene)	LGMD2WMDRCMTTPINCH-2PINCH2
Chromosome	2
Chromosome location	2q14.3
Summary	This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each do

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs754385302	G>C	Pathogenic	Coding sequence variant, intron variant, missense variant, non coding transcript variant, genic upstream transcript variant, upstream transcript variant
rs768056213	G>A,T	Pathogenic, uncertain-significance	Missense variant, upstream transcript variant, coding sequence variant, genic upstream transcript variant, intron variant, non coding transcript variant
rs869025562	A>G	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant

Show/Hide all (76)

miRTarBase ID	miRNA	Experiments	Reference
MIRT487031	hsa-miR-1827	PAR-CLIP	20371350
MIRT487029	hsa-miR-3184-5p	PAR-CLIP	20371350
MIRT487030	hsa-miR-423-5p	PAR-CLIP	20371350
MIRT487027	hsa-miR-25-5p	PAR-CLIP	20371350
MIRT487026	hsa-miR-6877-5p	PAR-CLIP	20371350
MIRT487025	hsa-miR-128-1-5p	PAR-CLIP	20371350
MIRT487024	hsa-miR-128-2-5p	PAR-CLIP	20371350
MIRT487032	hsa-miR-6770-5p	PAR-CLIP	23592263
MIRT487031	hsa-miR-1827	PAR-CLIP	23592263
MIRT487029	hsa-miR-3184-5p	PAR-CLIP	23592263
MIRT487030	hsa-miR-423-5p	PAR-CLIP	23592263
MIRT487028	hsa-miR-658	PAR-CLIP	23592263
MIRT487027	hsa-miR-25-5p	PAR-CLIP	23592263
MIRT487026	hsa-miR-6877-5p	PAR-CLIP	23592263
MIRT487025	hsa-miR-128-1-5p	PAR-CLIP	23592263
MIRT487024	hsa-miR-128-2-5p	PAR-CLIP	23592263
MIRT487031	hsa-miR-1827	PAR-CLIP	20371350
MIRT487029	hsa-miR-3184-5p	PAR-CLIP	20371350
MIRT487030	hsa-miR-423-5p	PAR-CLIP	20371350
MIRT487027	hsa-miR-25-5p	PAR-CLIP	20371350
MIRT487026	hsa-miR-6877-5p	PAR-CLIP	20371350
MIRT487025	hsa-miR-128-1-5p	PAR-CLIP	20371350
MIRT487024	hsa-miR-128-2-5p	PAR-CLIP	20371350
MIRT487032	hsa-miR-6770-5p	PAR-CLIP	23592263
MIRT487031	hsa-miR-1827	PAR-CLIP	23592263
MIRT487029	hsa-miR-3184-5p	PAR-CLIP	23592263
MIRT487030	hsa-miR-423-5p	PAR-CLIP	23592263
MIRT487028	hsa-miR-658	PAR-CLIP	23592263
MIRT487027	hsa-miR-25-5p	PAR-CLIP	23592263
MIRT487026	hsa-miR-6877-5p	PAR-CLIP	23592263
MIRT487025	hsa-miR-128-1-5p	PAR-CLIP	23592263
MIRT487024	hsa-miR-128-2-5p	PAR-CLIP	23592263
MIRT1109957	hsa-miR-1228	CLIP-seq
MIRT1109958	hsa-miR-1227	CLIP-seq
MIRT1109959	hsa-miR-3174	CLIP-seq
MIRT1109960	hsa-miR-3689d	CLIP-seq
MIRT1109961	hsa-miR-4252	CLIP-seq
MIRT1109962	hsa-miR-4254	CLIP-seq
MIRT1109963	hsa-miR-4265	CLIP-seq
MIRT1109964	hsa-miR-4292	CLIP-seq
MIRT1109965	hsa-miR-4296	CLIP-seq
MIRT1109966	hsa-miR-4308	CLIP-seq
MIRT1109967	hsa-miR-4322	CLIP-seq
MIRT1109968	hsa-miR-4417	CLIP-seq
MIRT1109969	hsa-miR-4481	CLIP-seq
MIRT1109970	hsa-miR-4537	CLIP-seq
MIRT1109971	hsa-miR-4658	CLIP-seq
MIRT1109972	hsa-miR-4671-5p	CLIP-seq
MIRT1109973	hsa-miR-4710	CLIP-seq
MIRT1109974	hsa-miR-4745-5p	CLIP-seq
MIRT1109975	hsa-miR-4758-5p	CLIP-seq
MIRT1109976	hsa-miR-4765	CLIP-seq
MIRT1109977	hsa-miR-4792	CLIP-seq
MIRT1109978	hsa-miR-563	CLIP-seq
MIRT1109960	hsa-miR-3689d	CLIP-seq
MIRT1109962	hsa-miR-4254	CLIP-seq
MIRT1109964	hsa-miR-4292	CLIP-seq
MIRT1109966	hsa-miR-4308	CLIP-seq
MIRT1109958	hsa-miR-1227	CLIP-seq
MIRT2261347	hsa-miR-1324	CLIP-seq
MIRT2261348	hsa-miR-1976	CLIP-seq
MIRT1109960	hsa-miR-3689d	CLIP-seq
MIRT1109961	hsa-miR-4252	CLIP-seq
MIRT1109962	hsa-miR-4254	CLIP-seq
MIRT2261349	hsa-miR-4267	CLIP-seq
MIRT1109964	hsa-miR-4292	CLIP-seq
MIRT1109966	hsa-miR-4308	CLIP-seq
MIRT1109971	hsa-miR-4658	CLIP-seq
MIRT2261350	hsa-miR-4722-3p	CLIP-seq
MIRT1109975	hsa-miR-4758-5p	CLIP-seq
MIRT1109976	hsa-miR-4765	CLIP-seq
MIRT1109978	hsa-miR-563	CLIP-seq
MIRT1109960	hsa-miR-3689d	CLIP-seq
MIRT1109962	hsa-miR-4254	CLIP-seq
MIRT1109964	hsa-miR-4292	CLIP-seq
MIRT1109966	hsa-miR-4308	CLIP-seq

Show/Hide all (27)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25416956, 32814053
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IEA
GO:0005911	Component	Cell-cell junction	IBA
GO:0005925	Component	Focal adhesion	HDA	21423176
GO:0005925	Component	Focal adhesion	IBA
GO:0005925	Component	Focal adhesion	IDA
GO:0005925	Component	Focal adhesion	IEA
GO:0007229	Process	Integrin-mediated signaling pathway	IEA
GO:0016020	Component	Membrane	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0045216	Process	Cell-cell junction organization	IBA
GO:0045216	Process	Cell-cell junction organization	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0061351	Process	Neural precursor cell proliferation	IEA
GO:0070161	Component	Anchoring junction	IEA
GO:0098609	Process	Cell-cell adhesion	IBA
GO:0098609	Process	Cell-cell adhesion	IEA
GO:1900026	Process	Positive regulation of substrate adhesion-dependent cell spreading	IBA
GO:1904055	Process	Negative regulation of cholangiocyte proliferation	IEA
GO:1990705	Process	Cholangiocyte proliferation	IEA
GO:2000178	Process	Negative regulation of neural precursor cell proliferation	IEA
GO:2000346	Process	Negative regulation of hepatocyte proliferation	IEA
GO:2001046	Process	Positive regulation of integrin-mediated signaling pathway	IBA
GO:2001046	Process	Positive regulation of integrin-mediated signaling pathway	IEA

MIM	HGNC	e!Ensembl
607908	16084	ENSG00000072163

Q7Z4I7

Protein name

LIM and senescent cell antigen-like-containing domain protein 2 (LIM-like protein 2) (Particularly interesting new Cys-His protein 2) (PINCH-2)

Protein 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. Plays a role in modulating cell spreading and migration. {ECO:0

PDB

3IXE

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00412	LIM	15 → 72	LIM domain	Domain
PF00412	LIM	76 → 131	LIM domain	Domain
PF00412	LIM	140 → 193	LIM domain	Domain
PF00412	LIM	198 → 253	LIM domain	Domain
PF00412	LIM	257 → 313	LIM domain	Domain

Sequence

MTGSNMSDALANAVCQRCQARFSPAERIVNSNGELYHEHCFVCAQCFRPFPEGLFYEFEG
RKYCEHDFQMLFAPCCGSCGEFIIGRVIKAMNNNWHPGCFRCELCDVELADLGFVKNAGR
HLCRPCHNREKAKGLGKYICQRCHLVIDEQPLMFRSDAYHPDHFNCTHCGKELTAEAREL
KGELYCLPCHDKMGVPICGACRRPIEGRVVNALGKQWHVEHFVCAKCEKPFLGHRHYEKK
GLAYCETHYNQLFGDVCYNCSHVIEGDVVSALNKAWCVSCFSCSTCNSKLTLKNKFVEFD
MKPVCKRCYEKFPLELKKRLKKLSELTSRKAQPKATDLNSA

Sequence length

341

Interactions

View interactions

	Reactome
			Cell-extracellular matrix interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive limb-girdle muscular dystrophy type 2W	Pathogenic; Likely pathogenic	rs869025562, rs1416116174, rs752012358	RCV000208564 RCV003340955 RCV003990272	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (26)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE LIMB-GIRDLE MUSCULAR DYSTROPHY	—	ClinGen	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Decreased total lymphocyte count	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Decreased total neutrophil count	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Germ cell tumor of testis	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIMB-GIRDLE MUSCULAR DYSTROPHY AUTOSOMAL RECESSIVE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIMS2-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (30)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Carcinoma	Carcinoma	BEFREE	20500520		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	36212176	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	BEFREE	25589244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	GENOMICS_ENGLAND_DG	25589244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Dilated	Cardiomyopathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	25346044		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Gestational	Gestational diabetes	Pubtator	35721735	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
LIMS2-related limb-girdle muscular dystrophy	Limb-Girdle Muscular Dystrophy	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant mesothelioma	Malignant Mesothelioma	BEFREE	20500520		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	16959213		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	20500520		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	25346044		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mesothelioma	Mesothelioma	BEFREE	20500520		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mesothelioma Malignant	Mesothelioma	Pubtator	20500520	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	BEFREE	25589244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	GENOMICS_ENGLAND_DG	25589244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	BEFREE	25589244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY, AUTOSOMAL RECESSIVE, WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	MUSCULAR DYSTROPHY WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	UNIPROT_DG	25589244		★★★★★ ★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY, AUTOSOMAL RECESSIVE, WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	MUSCULAR DYSTROPHY WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	ORPHANET_DG	25589244		★★★★★ ★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY, AUTOSOMAL RECESSIVE, WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	MUSCULAR DYSTROPHY WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	GENOMICS_ENGLAND_DG	25589244		★★★★★ ★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY, AUTOSOMAL RECESSIVE, WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	MUSCULAR DYSTROPHY WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY, AUTOSOMAL RECESSIVE, WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	MUSCULAR DYSTROPHY WITH CARDIOMYOPATHY AND TRIANGULAR TONGUE	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	BEFREE	31723057		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pulmonary Arterial Hypertension	Pulmonary arterial hypertension	Pubtator	35960497	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	16959213		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach Neoplasms	BEFREE	16959213		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach Neoplasms	LHGDN	16959213		★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	40755754	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

LIMS2 (LIM zinc finger domain containing 2)