ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.669G>C (p.Arg223Ser) (rs61749731)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000133184 SCV000513561 likely benign not specified 2017-04-05 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 RCV000645121 SCV000766863 benign Severe neonatal-onset encephalopathy with microcephaly 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000133184 SCV001362251 likely benign not specified 2019-04-10 criteria provided, single submitter clinical testing Variant summary: MECP2 c.633G>C (p.Arg211Ser) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0002 in 199776 control chromosomes (gnomAD). The observed variant frequency is approximately 24 fold of the estimated maximal expected allele frequency for a pathogenic variant in MECP2 causing Rett Syndrome phenotype (8.3e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.633G>C in individuals affected with Rett Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (1x likely benign, 1x benign). Based on the evidence outlined above, the variant was classified as likely benign.
RettBASE RCV000133184 SCV000188182 benign not specified 2013-12-05 no assertion criteria provided curation

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