ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.563C>G (p.Pro188Arg)

gnomAD frequency: 0.00005  dbSNP: rs61749701
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000133151 SCV000526561 likely benign not specified 2016-03-31 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587767 SCV000698541 benign not provided 2016-08-19 criteria provided, single submitter clinical testing Variant summary: The MECP2 c.527C>G (p.Pro176Arg) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 7/87892 control chromosomes at a frequency of 0.0000796, which is approximately 10 times the estimated maximal expected allele frequency of a pathogenic MECP2 variant (0.0000083), suggesting this variant is likely a benign polymorphism. This variant has been reported in multiple patients, an unaffected relative and healthy individuals as a polymorphism. In addition, multiple reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Invitae RCV002515931 SCV002936987 likely benign Severe neonatal-onset encephalopathy with microcephaly 2023-12-19 criteria provided, single submitter clinical testing
Centre for Population Genomics, CPG RCV003380475 SCV004098852 benign Rett syndrome 2023-08-14 criteria provided, single submitter curation This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria.Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders to the ACMG/AMP Variant Interpretation Guidelines VCEP 2.0 , this variant is classified as Benign. At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 2.0 (BA1). The variant is observed in at least 2 individuals with no features of Rett Syndrome (BS2).
RettBASE RCV000133151 SCV000188143 benign not specified 2010-03-10 no assertion criteria provided curation

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