ClinVar Miner

Submissions for variant NM_001161748.2(LIM2):c.380T>C (p.Leu127Pro)

gnomAD frequency: 0.00019  dbSNP: rs142111893
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001133659 SCV001293368 uncertain significance Cataract 19 multiple types 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Ambry Genetics RCV003163292 SCV003862802 uncertain significance Inborn genetic diseases 2023-02-23 criteria provided, single submitter clinical testing The c.506T>C (p.L169P) alteration is located in exon 4 (coding exon 3) of the LIM2 gene. This alteration results from a T to C substitution at nucleotide position 506, causing the leucine (L) at amino acid position 169 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV001133659 SCV004532540 uncertain significance Cataract 19 multiple types 2023-09-01 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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. ClinVar contains an entry for this variant (Variation ID: 894048). This variant has not been reported in the literature in individuals affected with LIM2-related conditions. This variant is present in population databases (rs142111893, gnomAD 0.2%). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 169 of the LIM2 protein (p.Leu169Pro).

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