ClinVar Miner

Submissions for variant NM_019066.5(MAGEL2):c.41C>A (p.Pro14Gln)

gnomAD frequency: 0.00038  dbSNP: rs769643348
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001355068 SCV002957882 likely benign not provided 2024-08-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV003284252 SCV003970360 likely benign Inborn genetic diseases 2023-03-31 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.
CeGaT Center for Human Genetics Tuebingen RCV001355068 SCV004131419 likely benign not provided 2024-07-01 criteria provided, single submitter clinical testing MAGEL2: BS1
Breakthrough Genomics, Breakthrough Genomics RCV001355068 SCV005193645 uncertain significance not provided criteria provided, single submitter not provided
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355068 SCV001549836 uncertain significance not provided no assertion criteria provided clinical testing The MAGEL2 p.Pro14Gln variant was not identified in the literature nor was it identified in ClinVar. The variant was identified in dbSNP (ID: rs769643348) and LOVD 3.0 (classified as a VUS). The variant was identified in control databases in 68 of 134210 chromosomes at a frequency of 0.0005067 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Other in 8 of 4052 chromosomes (freq: 0.001974), European (non-Finnish) in 59 of 61438 chromosomes (freq: 0.00096) and African in 1 of 15712 chromosomes (freq: 0.000064), but was not observed in the Latino, Ashkenazi Jewish, East Asian, European (Finnish) or South Asian populations. Computational analyses (PolyPhen-2, BLOSUM, MutationTaster) suggest that the variant will impact to the protein; however this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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