ClinVar Miner

Submissions for variant NM_001429.4(EP300):c.7111T>A (p.Ser2371Thr)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn RCV001250421 SCV001371846 likely pathogenic Menke-Hennekam syndrome 2 criteria provided, single submitter clinical testing Trio exome sequencing and analysis of the genes with the ten highest PEDIA values (PMID: 31164752) and of genes that could be associated with developmental delay (n=2539) revealed a probably pathogenic germ line variant in the EP300 gene (NM_001429.3) in this patient. The name of this missense variant is: c.7111T>A; p.(Ser2371Thr). This variant could not be detected in the parents, which is why it is highly probable that the patient developed it anew (de novo). In population-based and phenotype-based databases the above variant is not listed. The mutation prediction programs MutationTaster, PolyPhen-2 and PROVEAN classify the variant as a polymorphism, SIFT as "damaging"; the GADD score is 22.5. In order to assess the possible interference of the above variant with splice behavior, we used various programs for predicting splice locations and splice enhancers with the help of the Alamut software. The in silica analysis does not give any significant indication of a change in splice behavior. The ACMG classification of the variant is: probably pathogenic (class 4: PS2, PM2).

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