ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.1169C>T (p.Ala390Val) (rs201314910)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000132866 SCV000230271 benign not specified 2014-12-29 criteria provided, single submitter clinical testing
GeneDx RCV001090499 SCV000728724 likely benign not provided 2021-02-09 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 15737703)
Invitae RCV000694069 SCV000822496 likely benign Severe neonatal-onset encephalopathy with microcephaly 2020-03-30 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV001090499 SCV001246084 pathogenic not provided 2017-06-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000132866 SCV001362155 likely benign not specified 2019-05-31 criteria provided, single submitter clinical testing Variant summary: MECP2 c.1133C>T (p.Ala378Val) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 6.3e-05 in 175188 control chromosomes (2 hemizygotes). The observed variant frequency is approximately 7 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. c.1133C>T has been reported in the literature in one female individual affected with Rett Syndrome and patient's unaffected father (Fukuda_2005). This report suggests the variant does not associate with Rett Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as likely benign, and one laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.
RettBASE RCV000132866 SCV000187846 benign not specified 2010-03-10 no assertion criteria provided curation

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