De novo variation in EP300 gene cause Rubinstein-Taybi syndrome 2 in a Chinese family with severe early-onset high myopia

Abstract

Background: Rubinstein-Taybi syndrome (RSTS) is characterized by distinctive facial features, broad and often angulated thumbs and halluces, short stature, and moderate-to-severe intellectual disability, classified into two types RSTS1 (CREBBP-RSTS) and RSTS2 (EP300-RSTS). More often, the clinical features are inconclusive and the diagnosis of RSTS is established in a proband with identification of a heterozygous pathogenic variant in CREBBP or EP300 to confirm the diagnosis.

Methods: In this study, to describe an association between the clinical phenotype and the genotype of a RSTS2 patient who was initially diagnosed with severe early-onset high myopia (eoHM) from a healthy Chinese family, we tested the proband of this family by whole exome sequencing (WES) and further verified among other family members by Sanger sequencing. Real-time quantitative PCR was used to detect differences in the relative mRNA expression of candidate genes available in the proband and family members. Comprehensive ophthalmic tests as well as other systemic examinations were also performed on participants with various genotypes.

Results: Whole-exome sequencing revealed that the proband carried the heterozygous frameshift deletion variant c.3714_3715del (p.Leu1239Glyfs*3) in the EP300 gene, which was not carried by the normal parents and young sister as verified by Sanger sequencing, indicating that the variant was de novo. Real-time quantitative PCR showed that the mRNA expression of EP300 gene was lower in the proband than in other normal family members, indicating that such a variant caused an effect on gene function at the mRNA expression level. The variant was classified as pathogenic as assessed by the interpretation principles of HGMD sequence variants and ACMG guidelines. According to ACMG guidelines, the heterozygous frameshift deletion variant c.3714_3715del (p.Leu1239Glyfs*3) in the EP300 gene was more likely the pathogenic variant of this family with RSTS2.

Conclusions: Therefore, in this paper, we first report de novo heterozygous variation in EP300 causing eoHM-RSTS. Our study extends the genotypic spectrums for EP300-RSTS and better assists physicians in predicting, diagnosis, genetic counseling, eugenics guidance and gene therapy for EP300-RSTS.

Keywords: EP300 gene; Early onset high myopia; Phenotype; Rubinstein-Taybi syndrome 2.

Fig. 1

Photographs of the proband. (a) Photos of the face: low facial hairline (< 5 cm), high arched eyebrows, mildly downward palpebral fissures, long eyelashes, and convex nasal ridge with low-hanging columella. (b) Photos of hands and feet: slightly broad but not angulated thumbs and toes

Fig. 2

Fundus examination of the proband. (a) Fundus of both eyes: Fundus photography shows a diffuse chorioretinal atrophy and tessellation. (b) Optical Coherence tomography (OCT) of macula: no significant abnormalities. (c) OCT of optic disc: no significant abnormalities. (d) Vision Field: multiple central and peripheral scotomas

Fig. 3

Sequence analysis and identification of the novel mutations of EP300 in the affected family with autosomal-dominant RSTS. (a) Pedigree of the family. The filled black symbols represent the affected members and the arrow denotes the proband. (b) Sequence chromatograms of identified mutations. (c) The homology of amino acid sequences between human EP300 and other species. The amino acid at position 1239 (Leucine, L1239) is highly conserved among species. (d) Relative gene expression levels of EP300 in the affected family with autosomal-dominant RSTS:showing relative gene expression levels of EP300 of II-1(0.49) is lower than I-1(1.04),I-2(0.69) and II-2(0.97) and P value (II-1 : I-1) = 0.0011, P value (II-1 : I-2) = 0.0043, P value (II-1 : II-2) = 0.0036

Fig. 4

Work flow of WES analysis in this study. One variant in EP300 was selected out of 6 candidate variants based on the scores of mathematical predictions of mutational impact on proteins and its pathological impact as well. c.3714_3715del, which results in following amino acid substitution: (p.Leu1239Glyfs*3)