NM_001161748.2:c.388C>T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2PP3_ModeratePP5_Very_Strong
The NM_001161748.2(LIM2):c.388C>T(p.Arg130Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_001161748.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIM2 | ENST00000596399.2 | c.388C>T | p.Arg130Cys | missense_variant | Exon 4 of 5 | 1 | NM_001161748.2 | ENSP00000472090.2 | ||
LIM2 | ENST00000221973.7 | c.514C>T | p.Arg172Cys | missense_variant | Exon 4 of 5 | 1 | ENSP00000221973.2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461884Hom.: 0 Cov.: 38 AF XY: 0.00 AC XY: 0AN XY: 727240
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Cataract 19 multiple types Pathogenic:4
- -
This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 172 of the LIM2 protein (p.Arg172Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with autosomal dominant congenital cataracts (PMID: 32202185, 33078099). It has also been observed to segregate with disease in related individuals. This variant is also known as c.388C>T (p.R130C). ClinVar contains an entry for this variant (Variation ID: 625113). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. For these reasons, this variant has been classified as Pathogenic. -
- -
- -
Cataract Pathogenic:1
In this work, we identified a novel LIM2 mutation associated with autosomal dominant congenital membranous cataracts, which was known to be inherited by autosomal recessive pattern in all reported families with LIM2-mutant related cataract. Besides, morphological changes of the lens were characterized by macroscopically thin lenses, elongated axial length and microcosmically immature fiber cells which existed in the lens nucleus. Thus, we firstly suggest the impact of LIM2 during lens fiber cells differentiation, which could extend the understanding of the gene itself and give insight of the relationship between lens fiber cells differentiation and membranous cataract. All above are new finding and new concepts. -
LIM2-related disorder Pathogenic:1
The LIM2 c.514C>T variant is predicted to result in the amino acid substitution p.Arg172Cys. This variant was reported as a recurrent variant in multiple individuals with autosomal dominant cataract (reported as p.Arg130Cys in the literature, Berry et al 2020. PubMed ID: 32202185; Pei et al 2020. PubMed ID: 33078099; Wang et al 2021. PubMed ID: 33708862; Berry et al 2022. PubMed ID: 35736209; Fernández-Alcalde et al 2021. PubMed ID: 33923544). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -
not provided Pathogenic:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 28450710, 33708862, 33923544, 33078099, 32202185, 27535533) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at