ClinVar Miner

Submissions for variant NM_001161403.3(LIMS2):c.445G>A (p.Glu149Lys)

gnomAD frequency: 0.00013  dbSNP: rs148943578
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001242128 SCV001415195 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2W 2023-10-19 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 171 of the LIMS2 protein (p.Glu171Lys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with LIMS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 967259). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt LIMS2 protein function. 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.
Revvity Omics, Revvity RCV001242128 SCV003814609 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2W 2021-06-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV004639528 SCV005130416 uncertain significance not specified 2024-03-19 criteria provided, single submitter clinical testing The c.517G>A (p.E173K) alteration is located in exon 5 (coding exon 5) of the LIMS2 gene. This alteration results from a G to A substitution at nucleotide position 517, causing the glutamic acid (E) at amino acid position 173 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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