ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.1216_1251del (p.Glu406_Pro417del)

dbSNP: rs782746707
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Total submissions: 5
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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 RCV004797612 SCV005419051 likely benign Rett syndrome 2024-10-30 reviewed by expert panel curation The p.Glu394_Pro405del variant in MECP2 (NM_004992.4) is observed in at least 20 unaffected individuals (internal database - GeneDx; internal database - Invitae) (BS2). The p.Glu394_Pro405del variant is found in at least 2 patients with an alternate molecular basis of disease (internal database - GeneDx; internal database - Invitae) (BP5). The highest population minor allele frequency of the p.Glu394_Pro405del variant in MECP2 in gnomAD v4.1 is 0.00003691 in European (non-Finnish) population (not sufficient to meet BS1 criteria). In summary, the p.Glu394_Pro405del variant in MECP2 is classified as Likely Benign based on the ACMG/AMP criteria (BS2, BP5).
Molecular Diagnostics Lab, Nemours Children's Health, Delaware RCV000445565 SCV000537191 uncertain significance not specified 2015-07-15 criteria provided, single submitter clinical testing
GeneDx RCV000766764 SCV000582995 uncertain significance not provided 2021-04-01 criteria provided, single submitter clinical testing In-frame deletion of 12 amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV001267433 SCV001445614 uncertain significance Inborn genetic diseases 2018-07-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001339351 SCV001533091 uncertain significance Severe neonatal-onset encephalopathy with microcephaly 2024-02-22 criteria provided, single submitter clinical testing This variant, c.1180_1215del, results in the deletion of 12 amino acid(s) of the MECP2 protein (p.Glu394_Pro405del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs782746707, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with MECP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 393491). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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