PDLIM4 (PDZ and LIM domain 4)

Gene

• Entrez ID: 8572
• Gene name: PDZ and LIM domain 4
• Gene symbol: PDLIM4
• Synonyms (NCBI Gene): RIL
• Chromosome: 5
• Chromosome location: 5q31.1
• Summary: This gene encodes a protein which may be involved in bone development. Mutations in this gene are associated with susceptibility to osteoporosis. [provided by RefSeq, Nov 2009]

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018921	hsa-miR-335-5p	Microarray	18185580
MIRT1222217	hsa-miR-125a-5p	CLIP-seq
MIRT1222218	hsa-miR-125b	CLIP-seq
MIRT1222219	hsa-miR-3653	CLIP-seq
MIRT1222220	hsa-miR-3658	CLIP-seq
MIRT1222221	hsa-miR-4300	CLIP-seq
MIRT1222222	hsa-miR-4319	CLIP-seq
MIRT1222223	hsa-miR-4432	CLIP-seq
MIRT1222224	hsa-miR-4446-5p	CLIP-seq
MIRT1222225	hsa-miR-4690-5p	CLIP-seq
MIRT1222226	hsa-miR-4732-3p	CLIP-seq
MIRT1222227	hsa-miR-4755-5p	CLIP-seq
MIRT1222228	hsa-miR-499-5p	CLIP-seq
MIRT1222229	hsa-miR-670	CLIP-seq
MIRT1222230	hsa-miR-920	CLIP-seq
MIRT2064360	hsa-miR-1973	CLIP-seq
MIRT2064361	hsa-miR-3679-3p	CLIP-seq
MIRT2064362	hsa-miR-507	CLIP-seq
MIRT2064363	hsa-miR-557	CLIP-seq
MIRT2064360	hsa-miR-1973	CLIP-seq
MIRT2064361	hsa-miR-3679-3p	CLIP-seq
MIRT2064362	hsa-miR-507	CLIP-seq
MIRT2064363	hsa-miR-557	CLIP-seq
MIRT2590723	hsa-miR-3168	CLIP-seq
MIRT1222223	hsa-miR-4432	CLIP-seq
MIRT1222224	hsa-miR-4446-5p	CLIP-seq
MIRT1222227	hsa-miR-4755-5p	CLIP-seq
MIRT1222228	hsa-miR-499-5p	CLIP-seq
MIRT1222229	hsa-miR-670	CLIP-seq
MIRT2590723	hsa-miR-3168	CLIP-seq
MIRT1222223	hsa-miR-4432	CLIP-seq
MIRT1222224	hsa-miR-4446-5p	CLIP-seq
MIRT1222227	hsa-miR-4755-5p	CLIP-seq
MIRT1222228	hsa-miR-499-5p	CLIP-seq
MIRT1222229	hsa-miR-670	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001725	Component	Stress fiber	IBA
GO:0001725	Component	Stress fiber	IDA	21636573
GO:0003779	Function	Actin binding	IBA
GO:0005515	Function	Protein binding	IPI	10826496, 19307596, 21636573, 32296183
GO:0005634	Component	Nucleus	IDA	10826496, 21636573
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IDA	21636573
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IDA	21636573
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IDA
GO:0005912	Component	Adherens junction	IBA
GO:0007507	Process	Heart development	IBA
GO:0015629	Component	Actin cytoskeleton	IDA
GO:0016020	Component	Membrane	IEA
GO:0019903	Function	Protein phosphatase binding	IEA
GO:0019903	Function	Protein phosphatase binding	IPI	19307596
GO:0030018	Component	Z disc	IBA
GO:0030027	Component	Lamellipodium	IDA	10826496
GO:0030027	Component	Lamellipodium	IEA
GO:0030036	Process	Actin cytoskeleton organization	IBA
GO:0030036	Process	Actin cytoskeleton organization	IDA	21636573
GO:0031901	Component	Early endosome membrane	IEA
GO:0031905	Component	Early endosome lumen	ISS
GO:0031941	Component	Filamentous actin	IBA
GO:0031941	Component	Filamentous actin	IDA	10826496
GO:0034777	Component	Recycling endosome lumen	ISS
GO:0042803	Function	Protein homodimerization activity	IDA	25158098
GO:0042995	Component	Cell projection	IEA
GO:0043005	Component	Neuron projection	IEA
GO:0043197	Component	Dendritic spine	IEA
GO:0043197	Component	Dendritic spine	ISS
GO:0045202	Component	Synapse	IEA
GO:0045211	Component	Postsynaptic membrane	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	19307596
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0051371	Function	Muscle alpha-actinin binding	IBA
GO:0051393	Function	Alpha-actinin binding	IPI	20120020
GO:0055038	Component	Recycling endosome membrane	IEA
GO:0061061	Process	Muscle structure development	IBA
GO:0098976	Process	Excitatory chemical synaptic transmission	ISS

Other IDs

• MIM: 603422
• HGNC: 16501
• e!Ensembl: ENSG00000131435

Protein

• UniProt ID: P50479
• Protein name: PDZ and LIM domain protein 4 (LIM protein RIL) (Reversion-induced LIM protein)
• Protein function: [Isoform 1]: Suppresses SRC activation by recognizing and binding to active SRC and facilitating PTPN13-mediated dephosphorylation of SRC 'Tyr-419' leading to its inactivation. Inactivated SRC dissociates from this protein allowing the initiatio
• PDB: 2EEG, 2V1W, 4Q2O
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00595	PDZ	4 → 81	PDZ domain	Domain
  PF15936	DUF4749	147 → 228	Domain of unknown function (DUF4749)	Family
  PF00412	LIM	255 → 309	LIM domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: [Isoform 2]: Found in brain. {ECO:0000269|PubMed:9573374}.
• Sequence:

  MPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELM
  THLEAQNRIKGCHDHLTLSVSRPEGRSWPSAPDDSKAQAHRIHIDPEIQDGSPTTSRRPS
  GTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMSTLHVSPPPSADPARGLPRSR
  DCRVDLGSEVYRMLREPAEPVAAEPKQSGSFRYLQGMLEAGEGGDWPGPGGPRNLKPTAS
  KLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHPECFMCSDCGLNLKQRGYFFLDERL
  YCESHAKARVKPPEGYDVVAVYPNAKVELV

• Sequence length: 330

Pathways

KEGG:

Cytoskeleton in muscle cells

Associated diseases

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATOPIC ECZEMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 15	risk factor	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPOROSIS	—	CTD, ClinVar, Disgenet CTD, ClinVar, Disgenet CTD, ClinVar, Disgenet CTD, ClinVar, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYCYSTIC OVARY SYNDROME	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autoimmune Diseases	Autoimmune Diseases	BEFREE	30307322		★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar Disorder	BEFREE	23031404		★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar disorder	Pubtator	23031404	Associate	★☆☆☆☆ Found in Text Mining only
Bone Marrow Diseases	Bone marrow diseases	Pubtator	30578378	Associate	★☆☆☆☆ Found in Text Mining only
Breast adenocarcinoma	Breast Adenocarcinoma	BEFREE	24657059		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	22695491		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	17764565, 22695491, 36936167, 38235137	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	20154727	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	31376371		★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	29126926		★☆☆☆☆ Found in Text Mining only
Cervix carcinoma	Cervix carcinoma	BEFREE	29126926		★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	17332327, 21060154		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	19307596	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	35456975	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	17332327		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	21060154		★☆☆☆☆ Found in Text Mining only
Liver neoplasms	Liver neoplasms	BEFREE	21060154		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung Neoplasms	CTD_human_DG	27935865		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	20642860	Associate	★☆☆☆☆ Found in Text Mining only
Malignant mesothelioma	Malignant Mesothelioma	BEFREE	24336325		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	22695491		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	CTD_human_DG	27935865		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	31376371		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	16489065, 17975004, 19212833, 19623543		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	17332327, 18725933		★☆☆☆☆ Found in Text Mining only
Malignant tumor of cervix	Cervical Tumor	BEFREE	29126926		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	17332327		★☆☆☆☆ Found in Text Mining only
MYELODYSPLASTIC SYNDROME	Myelodysplastic Syndrome	BEFREE	17332327		★☆☆☆☆ Found in Text Mining only
Myeloid Leukemia, Chronic	Myeloid Leukemia	BEFREE	21760961		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	11420696, 16489065, 19212833, 19623543, 22695491, 29137356, 31376371		★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	BEFREE	12908099		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteoporosis	Osteoporosis	LHGDN	12908099		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteoporosis	Osteoporosis	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteoporosis	Osteoporosis	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteoporosis, Age-Related	Osteoporosis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Osteoporosis, Senile	Osteoporosis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	31376371		★☆☆☆☆ Found in Text Mining only
Polycystic Ovary Syndrome	Polycystic Ovary Syndrome	CTD_human_DG	21411543		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Post-Traumatic Osteoporosis	Osteoporosis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	16489065, 17975004, 19212833, 19623543		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	19229700, 21694441	Associate	★☆☆☆☆ Found in Text Mining only
Sclerocystic Ovaries	Sclerocystic Ovaries	CTD_human_DG	21411543		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	22154084		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	35982735	Associate	★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasm	Thyroid Neoplasm	BEFREE	31006665		★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasms	Thyroid cancer	Pubtator	31006665	Associate	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	17764565		★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	17764565	Associate	★☆☆☆☆ Found in Text Mining only