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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	55679
Gene name Gene Name - the full gene name approved by the HGNC.	LIM zinc finger domain containing 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	LIMS2
Synonyms (NCBI Gene) Gene synonyms aliases	LGMD2W, MDRCMTT, PINCH-2, PINCH2
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q14.3
Summary Summary of gene provided in NCBI Entrez Gene.	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

Protein

UniProt ID

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

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Limb-girdle muscular dystrophy	Autosomal recessive limb-girdle muscular dystrophy type 2W	rs869025562	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Diabetes	Type 2 diabetes	N/A	N/A	GWAS

Show/Hide Text Mining Associations (7)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Carcinoma Hepatocellular	Associate	36212176
Cell Transformation Neoplastic	Associate	36212176
Diabetes Gestational	Associate	35721735
Mesothelioma Malignant	Stimulate	20500520
Neoplasms	Associate	20500520, 40755754
Pulmonary Arterial Hypertension	Associate	35960497
Urinary Bladder Neoplasms	Associate	40755754

LIMS2 (LIM zinc finger domain containing 2)