ClinVar Miner

Submissions for variant NM_004992.3(MECP2):c.1160C>T (p.Pro387Leu) (rs63390262)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224689 SCV000280687 likely benign not provided 2015-05-08 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Integrated Genetics/Laboratory Corporation of America RCV000608016 SCV000698534 likely benign not specified 2017-11-22 criteria provided, single submitter clinical testing Variant summary: The MECP2 c.1160C>T (p.Pro387Leu) variant involves the alteration of a conserved nucleotide. 3/5 in silico tools predict a damaging outcome for this variant. This variant was found in 17/186675 control chromosomes (gnomAD) at a frequency of 0.0000911, which is approximately 11 times the estimated maximal expected allele frequency of a pathogenic MECP2 variant (0.0000083), suggesting this variant is likely a benign polymorphism. The variant of interest has been reported via a publication in a homozygous female suspected to have Rett syndrome (Bhanushali_2016), however, her father also carried the variant and was stated to be mentally normal. In addition, one clinical diagnostic laboratory classified this variant as likely benign. Taken together, this variant is classified as likely benign.
GeneDx RCV000608016 SCV000728726 likely benign not specified 2018-02-05 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 RCV000224689 SCV000766872 benign not provided 2019-02-14 criteria provided, single submitter clinical testing
RettBASE RCV000132908 SCV000187889 uncertain significance Mental retardation, X-linked, syndromic 13 2002-04-10 no assertion criteria provided curation

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