ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.660G>A (p.Gln220=) (rs142234258)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000656957 SCV000231085 uncertain significance not provided 2015-01-06 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000242887 SCV000311178 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000374157 SCV000373034 likely benign Glycogen storage disease, type V 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000656957 SCV000565454 uncertain significance not provided 2018-07-11 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the PYGM gene. The c.660 G>A variant has been previously reported in an individual with both McArdle disease and multiple sclerosis (Zoccolella., et al 2015). This individual harbored an additional PYGM variant and histoenzymatic analysis revealed myophosphorylase deficiency that was confirmed by analysis of muscle homogenate. The c.660 G>A variant is observed in 185/30782 (0.6%) alleles from individuals of South Asian background (Lek et al., 2016). Several in-silico splice prediction models predict that c.660 G>A damages the natural splice donor site of intron 5 and may 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. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Counsyl RCV000374157 SCV000800207 uncertain significance Glycogen storage disease, type V 2018-05-24 criteria provided, single submitter clinical testing
Invitae RCV000374157 SCV000831281 benign Glycogen storage disease, type V 2020-12-04 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000656957 SCV001148316 uncertain significance not provided 2021-01-01 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV000374157 SCV001737303 uncertain significance Glycogen storage disease, type V 2021-06-10 criteria provided, single submitter clinical testing
Natera, Inc. RCV000374157 SCV001457728 uncertain significance Glycogen storage disease, type V 2020-04-14 no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000656957 SCV001799909 uncertain significance not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000656957 SCV001809079 uncertain significance not provided no assertion criteria provided clinical testing

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