LIM2
Basic information
Region (hg38): 19:51379909-51387974
Links
Phenotypes
GenCC
Source:
- 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:
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
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 | 14 | |||||
missense | 31 | 32 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 2 | 2 | ||||
non coding | 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) | ||
19-51380508-C-T | Cataract 19 multiple types | Uncertain significance (Jul 10, 2024) | ||
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 (Nov 27, 2023) | ||
19-51380580-G-A | Uncertain significance (Aug 07, 2024) | |||
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) |
GnomAD
Source:
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:
- 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