ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.1787A>G (p.Asn596Ser) (rs150622626)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000675629 SCV000345754 uncertain significance not provided 2016-09-20 criteria provided, single submitter clinical testing
GeneDx RCV000675629 SCV000618336 uncertain significance not provided 2018-12-04 criteria provided, single submitter clinical testing The N596S (c.1787 A>G) variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The N596S variant is observed in 23/10400 (0.2%) alleles from individuals of African background in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The N596S variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is conserved in mammals. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Several in-silico splice prediction models predict that the c.1787 A>G variant that encodes N596S for creates a cryptic donor site which may supplant the natural donor site and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000675629 SCV000801330 uncertain significance not provided 2017-06-15 no assertion criteria provided clinical testing

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