ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.550C>A (p.Pro184Thr)

dbSNP: rs61748426
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001193434 SCV001362255 likely benign not specified 2019-02-07 criteria provided, single submitter clinical testing Variant summary: MECP2 c.514C>A (p.Pro172Thr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.1e-05 in 178447 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.514C>A in individuals affected with Rett Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. The variant was reported to be found in an internal unaffected male sample, providing supporting evidence for a benign role. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely benign.
Invitae RCV001344042 SCV001538071 uncertain significance Severe neonatal-onset encephalopathy with microcephaly 2022-05-15 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 172 of the MECP2 protein (p.Pro172Thr). This variant is present in population databases (no rsID available, gnomAD 0.004%). 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: 928877). 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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