ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.626C>T (p.Thr209Met)

gnomAD frequency: 0.00064  dbSNP: rs61749714
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000169928 SCV000170219 benign not specified 2013-03-18 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.
Eurofins Ntd Llc (ga) RCV000169928 SCV000230273 benign not specified 2014-08-15 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000169928 SCV000247980 benign not specified 2013-02-08 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000224787 SCV000281658 likely benign not provided 2014-12-05 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000225683 SCV000282492 benign Rett syndrome 2015-10-02 criteria provided, single submitter clinical testing The observed allele frequency of this variant in the large and diverse ExAC cohort is 48/87676 (1/1827) with 20 hemizygotes, suggesting that it is a benign polymorphism. The variant is classified as a polymorphism/not disease-causing in the literature, and has been shown to not co-segregate with disease in at least 2 families. Variant was observed in cis with pathogenic MECP2 variants (c.473C>T/p.T158M, c.916C>T/p.R306C) in multiple RTT patients.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000169928 SCV000539603 likely benign not specified 2016-03-28 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC: 0.1% (15/10125) South Asian chromosomes. Duplication of gene associated with intellectual disability, hypotonia, seizures, spasticity. SNVs associated with Rett syndrome.
Invitae RCV001086086 SCV000556731 benign Severe neonatal-onset encephalopathy with microcephaly 2024-01-30 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000626211 SCV000746855 likely benign X-linked intellectual disability-psychosis-macroorchidism syndrome 2017-12-18 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000225683 SCV000746927 likely benign Rett syndrome 2017-12-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV002316387 SCV000851917 benign Inborn genetic diseases 2017-08-04 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Mendelics RCV000225683 SCV001142086 likely benign Rett syndrome 2019-05-28 criteria provided, single submitter clinical testing
Centre for Population Genomics, CPG RCV000225683 SCV004098735 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 Specifications 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 RCV000169928 SCV000188161 benign not specified 2013-06-12 no assertion criteria provided curation

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