ClinVar Miner

Submissions for variant NM_002294.3(LAMP2):c.472A>G (p.Thr158Ala)

gnomAD frequency: 0.00003  dbSNP: rs138374063
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000037419 SCV000061076 uncertain significance not specified 2012-07-06 criteria provided, single submitter clinical testing Variant classified as Uncertain Significance - Favor Benign. The Thr158Ala varia nt in LAMP2 has been identified in 2/6727 European American chromosomes from a b road population by the NHLBI Exome Sequencing Project (http://evs.gs.washington. edu/EVS; dbSNP rs138374063). Threonine (Thr) at position 158 is not conserved in mammals or evolutionarily distant species and elephant carries an alanine (Ala; this variant), suggesting that this change may be tolerated. In addition, compu tational analyses (biochemical amino acid properties, AlignGVGD, PolyPhen2, and SIFT) suggest that this variant may not impact the protein, though this informat ion is not predictive enough to rule out pathogenicity. In summary, the frequenc y of this variant and lack of amino acid conservation suggests that it may be mo re likely benign, but additional information is needed to fully assess its clini cal significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV000547615 SCV000636864 likely benign Danon disease 2025-01-12 criteria provided, single submitter clinical testing
GeneDx RCV000675449 SCV001989013 uncertain significance not provided 2023-08-28 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 27532257)
Ambry Genetics RCV002336129 SCV002635911 likely benign Cardiovascular phenotype 2022-02-14 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute RCV000037419 SCV006070143 likely benign not specified 2025-04-09 criteria provided, single submitter clinical testing BS1, BP1, BP4
Mayo Clinic Laboratories, Mayo Clinic RCV000675449 SCV000801131 uncertain significance not provided 2017-11-13 no assertion criteria provided clinical testing

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