LIM2

lens intrinsic membrane protein 2

Basic information

Region (hg38): 19:51379908-51387974

Links

ENSG00000105370 ∙ NCBI:3982 ∙ OMIM:154045 ∙ HGNC:6610 ∙ Uniprot:P55344 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• total early-onset cataract (Supportive), mode of inheritance: AD
• cataract 19 multiple types (Limited), mode of inheritance: AR
• cataract 19 multiple types (Definitive), mode of inheritance: AR
• cataract 19 multiple types (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 19. multiple types	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	11917274; 32202185; 33708862; 35736209

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LIM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIM2 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			7	7		14
missense		1	31			32
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2			2
non coding			8	4	10	22
Total	0	1	48	11	10

Variants in LIM2

This is a list of pathogenic ClinVar variants found in the LIM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51379910-A-G		Cataract 19 multiple types	Uncertain significance (Jan 13, 2018)
19-51379956-T-C		Cataract 19 multiple types	Uncertain significance (Jan 13, 2018)
19-51379983-G-C		Cataract 19 multiple types	Uncertain significance (Jan 13, 2018)
19-51380143-C-T		Cataract 19 multiple types	Uncertain significance (Jan 13, 2018)
19-51380221-G-A		Cataract 19 multiple types • Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
19-51380223-C-T		Cataract 19 multiple types • Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
19-51380233-G-A		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
19-51380236-C-T		Cataract 19 multiple types • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jun 16, 2024)
19-51380239-G-A		Cataract 19 multiple types	Uncertain significance (Nov 26, 2019)
19-51380240-G-A		LIM2-related disorder	Likely benign (Mar 25, 2019)
19-51380262-C-T		Cataract 19 multiple types	Pathogenic (Mar 10, 2016)
19-51380277-G-T		Cataract 19 multiple types	Likely benign (May 03, 2022)
19-51380473-G-A			Benign (Jun 29, 2018)
19-51380486-C-G		Cataract 19 multiple types	Benign (Jan 05, 2024)
19-51380492-T-A		Cataract 19 multiple types	Likely benign (Dec 09, 2023)
19-51380496-C-T		Cataract 19 multiple types	Uncertain significance (Jan 13, 2018)
19-51380516-G-A		Inborn genetic diseases	Uncertain significance (Jun 18, 2024)
19-51380525-A-G		Inborn genetic diseases • Cataract 19 multiple types	Uncertain significance (May 23, 2023)
19-51380545-G-T		Cataract 19 multiple types	Uncertain significance (Jul 19, 2017)
19-51380576-C-T		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
19-51380577-G-A		Cataract • Cataract 19 multiple types • LIM2-related disorder	Pathogenic/Likely pathogenic (Jan 17, 2024)
19-51380580-G-A			Uncertain significance (Sep 07, 2023)
19-51380585-A-G		Cataract 19 multiple types • Inborn genetic diseases	Uncertain significance (Sep 01, 2023)
19-51380596-G-A		Cataract 19 multiple types	Likely benign (Jul 26, 2021)
19-51380608-G-A		Cataract 19 multiple types	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIM2	protein_coding	protein_coding	ENST00000221973	4	8052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000678	0.761	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.667	158	136	1.16	0.0000101	1382
Missense in Polyphen		67	64	1.0469		624
Synonymous	-0.308	55	52.2	1.05	0.00000345	450
Loss of Function	0.985	6	9.23	0.650	4.06e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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.

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.181
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.210
• hipred: N
• hipred_score: 0.170
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lim2
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: lens development in camera-type eye;cell-cell junction assembly
• Cellular component: plasma membrane;integral component of membrane;cell junction;vesicle
• Molecular function: structural constituent of eye lens