ClinVar Miner

Submissions for variant NM_002294.2(LAMP2):c.517G>A (p.Val173Ile) (rs141574558)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000037420 SCV000532767 likely benign not specified 2016-10-14 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000638586 SCV000760118 likely benign Danon disease 2017-12-29 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000037420 SCV000061077 uncertain significance not specified 2014-02-28 criteria provided, single submitter clinical testing Variant classified as Uncertain Significance - Favor Benign. The Val173Ile varia nt in LAMP2 has been previously reported by our laboratory in 2 individuals with HCM who were also carriers of a pathogenic variant in another HCM gene. It has also been identified in 2/6728 European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu; dbSNP rs141574558). Computati onal prediction tools suggest that this variant may not impact the protein, thou gh this information is not predictive enough to rule out pathogenicity. Valine ( Val) at position 173 is not conserved in mammals or evolutionarily distant speci es, with one mammal (Chinese tree shrew) and some fish having this variant (Ile) at this position, further supporting that a change at this position may be tole rated. Furthermore, nearly all disease-causing variants in LAMP2 have been trunc ating, while this is a missense variant. In summary, although this data supports that the Val173Ile variant may be more likely benign, additional studies are ne eded to fully assess its clinical significance.

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