ClinVar Miner

Submissions for variant NM_002294.3(LAMP2):c.49G>A (p.Val17Ile)

dbSNP: rs777718603
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001997230 SCV002236511 uncertain significance Danon disease 2024-11-11 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 17 of the LAMP2 protein (p.Val17Ile). This variant is present in population databases (rs777718603, gnomAD 0.02%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with LAMP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1448795). 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 tolerated. 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.
Ambry Genetics RCV002334962 SCV002640674 uncertain significance Cardiovascular phenotype 2022-08-08 criteria provided, single submitter clinical testing The p.V17I variant (also known as c.49G>A), located in coding exon 1 of the LAMP2 gene, results from a G to A substitution at nucleotide position 49. The valine at codon 17 is replaced by isoleucine, an amino acid with highly similar properties. Based on data from gnomAD, the A allele has an overall frequency of 0.0011% (2/182167) total alleles studied, with 1 hemizygote(s) observed. The highest observed frequency was 0.0153% (2/13095) of African alleles. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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