LIM2 (lens intrinsic membrane protein 2)

Gene

• Entrez ID: 3982
• Gene name: Lens intrinsic membrane protein 2
• Gene symbol: LIM2
• Synonyms (NCBI Gene): CTRCT19, MP17, MP19
• Chromosome: 19
• Chromosome location: 19q13.41
• Summary: This gene encodes an eye lens-specific protein found at the junctions of lens fiber cells, where it may contribute to cell junctional organization. It acts as a receptor for calmodulin, and may play an important role in both lens development and cataracto

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121913555	A>C	Pathogenic	Coding sequence variant, missense variant
rs869312732	C>T	Pathogenic	Missense variant, coding sequence variant
rs1568480054	G>A	Pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018500	hsa-miR-335-5p	Microarray	18185580
MIRT1109399	hsa-miR-4514	CLIP-seq
MIRT1109400	hsa-miR-4645-5p	CLIP-seq
MIRT1109401	hsa-miR-4652-5p	CLIP-seq
MIRT1109402	hsa-miR-4673	CLIP-seq
MIRT1109403	hsa-miR-4692	CLIP-seq
MIRT1109404	hsa-miR-4722-3p	CLIP-seq
MIRT1109405	hsa-miR-4755-3p	CLIP-seq
MIRT1109406	hsa-miR-483-5p	CLIP-seq
MIRT2030424	hsa-miR-3135	CLIP-seq
MIRT2030425	hsa-miR-4433	CLIP-seq
MIRT2030426	hsa-miR-665	CLIP-seq
MIRT2030424	hsa-miR-3135	CLIP-seq
MIRT2030425	hsa-miR-4433	CLIP-seq
MIRT2030426	hsa-miR-665	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002088	Process	Lens development in camera-type eye	IEA
GO:0005212	Function	Structural constituent of eye lens	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0007043	Process	Cell-cell junction assembly	NAS	2584203
GO:0016020	Component	Membrane	IEA
GO:0030054	Component	Cell junction	NAS	2584203
GO:0031982	Component	Vesicle	IEA
GO:0043010	Process	Camera-type eye development	IEA

Other IDs

• MIM: 154045
• HGNC: 6610
• e!Ensembl: ENSG00000105370

Protein

• UniProt ID: P55344
• Protein name: Lens fiber membrane intrinsic protein (MP18) (MP19) (MP20)
• Protein function: Present in the thicker 16-17 nm junctions of mammalian lens fiber cells, where it may contribute to cell junctional organization. Acts as a receptor for calmodulin. May play an important role in both lens development and cataractogenesis.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00822	PMP22_Claudin	1 → 157	PMP-22/EMP/MP20/Claudin family	Family

• Tissue specificity: TISSUE SPECIFICITY: Eye lens specific. {ECO:0000269|PubMed:12107413}.
• Sequence:

  MYSFMGGGLFCAWVGTILLVVAMATDHWMQYRLSGSFAHQGLWRYCLGNKCYLQTDSIAY
  WNATRAFMILSALCAISGIIMGIMAFAHQPTFSRISRPFSAGIMFFSSTLFVVLALAIYT
  GVTVSFLGRRFGDWRFSWSYILGWVAVLMTFFAGIFYMCAYRVHECRRLSTPR

• Sequence length: 173

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cataract	Likely pathogenic; Pathogenic	rs1568480054	RCV000766206	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cataract 19 multiple types	Pathogenic; Likely pathogenic	rs869312732, rs121913555, rs1568480054	RCV000209996 RCV000015430 RCV001212191	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
LIM2-related disorder	Likely pathogenic; Pathogenic	rs1568480054	RCV003947967	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CATARACT 19 MULTIPLE TYPE S	—	ClinVar, GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CATARACT 19, MULTIPLE TYPE S	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL CATARACT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL TOTAL CATARACT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cortical pulverulent cataract	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOTAL EARLY-ONSET CATARACT	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adrenocortical Carcinoma Hereditary	Adrenocortical carcinoma	Pubtator	38178039	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	BEFREE	11917274, 18596884		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cataract	Cataract	CTD_human_DG	11917274		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cataract	Cataract	LHGDN	18596884		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cataract	Cataract	Pubtator	18596884, 33923544, 35736209, 38178039	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cataract	Cataract	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CATARACT 19, MULTIPLE TYPES	Cataract	UNIPROT_DG	11917274		★☆☆☆☆ Found in Text Mining only
CATARACT 19, MULTIPLE TYPES	Cataract	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
CATARACT 19, MULTIPLE TYPES	Cataract	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
CATARACT 19, MULTIPLE TYPES	Cataract	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Congenital cataract	Congenital Cataract	BEFREE	18596884, 27814360		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital cataract	Congenital Cataract	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital total cataract	Congenital Cataract	ORPHANET_DG	18596884		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cortical pulverulent cataract	Cortical cataract	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cortical pulverulent cataract	Cortical cataract	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fatty Liver	Fatty Liver	BEFREE	29301219		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	22983390, 28055976	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	28055976		★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	BEFREE	12379840		★☆☆☆☆ Found in Text Mining only
Milroy Disease	Milroy Disease	BEFREE	9920853		★☆☆☆☆ Found in Text Mining only
Myofibrillar Myopathy	Myofibrillar myopathy	Pubtator	22094483	Associate	★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Peripheral nervous system disease	Pubtator	22094483	Associate	★☆☆☆☆ Found in Text Mining only
Presenile cataract	Presenile Cataract	BEFREE	11917274		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	15692560	Associate	★☆☆☆☆ Found in Text Mining only
Pseudoaphakia	Cataract	CTD_human_DG	11917274		★☆☆☆☆ Found in Text Mining only
Reducing-body myopathy	Reducing body myopathy	BEFREE	20571991		★☆☆☆☆ Found in Text Mining only
Respiratory Distress Syndrome, Adult	Respiratory Distress Syndrome	CTD_human_DG	25070658		★☆☆☆☆ Found in Text Mining only
Total early-onset cataract	Cataract	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vision Disorders	Visual disorder	Pubtator	18596884	Associate	★☆☆☆☆ Found in Text Mining only