ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.260C>T (p.Pro87Leu)

gnomAD frequency: 0.00003  dbSNP: rs267608440
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel RCV000195208 SCV002769693 benign Rett syndrome 2022-10-11 reviewed by expert panel curation The allele frequency of the p.Pro75Leu variant in MECP2 (NM_004992.3) is 0.038% in the Other sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). In summary, the p.Pro75Leu variant in MECP2 is classified as Benign based on the ACMG/AMP criteria (BA1).
Genetic Services Laboratory, University of Chicago RCV000195208 SCV000247960 uncertain significance Rett syndrome 2016-09-23 criteria provided, single submitter clinical testing
Invitae RCV001414793 SCV001616936 likely benign Severe neonatal-onset encephalopathy with microcephaly 2024-01-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002515929 SCV003546796 uncertain significance Inborn genetic diseases 2021-02-19 criteria provided, single submitter clinical testing The c.224C>T (p.P75L) alteration is located in exon 3 (coding exon 2) of the MECP2 gene. This alteration results from a C to T substitution at nucleotide position 224, causing the proline (P) at amino acid position 75 to be replaced by a leucine (L). The p.P75L alteration is predicted to be deleterious by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Centre for Population Genomics, CPG RCV000195208 SCV004232219 benign Rett syndrome 2024-01-15 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 Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 3.0, 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 3.0 (BA1).
PreventionGenetics, part of Exact Sciences RCV003927411 SCV004744533 likely benign MECP2-related condition 2023-05-03 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
RettBASE RCV000133035 SCV000188023 uncertain significance not specified 2011-02-15 no assertion criteria provided curation

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