A Novel Intronic Mutation in MBD5 Results in Autosomal Dominant Intellectual Disability Type 1 due to Abnormal Splicing

TL;DR

A new mutation in the MBD5 gene causes abnormal mRNA splicing, leading to intellectual disability and expanding the known pathogenic variants for this condition.

Contribution

The study identifies a novel intronic mutation in MBD5 that causes abnormal splicing and expands the mutation database for Autosomal Dominant Intellectual Disability Type 1.

Findings

The c.114‐13A>G mutation in MBD5 leads to two types of aberrant mRNA splicing.

The mutation results in changes to the protein's spatial structure and electrostatic potential.

The mutation meets ACMG criteria PS2 and PS3, indicating it is pathogenic.

Abstract

We identified a novel variant in MBD5 located within intron 6: c.114‐13A>G (NM_018328.5) in a family with a patient presenting intellectual disability. This variant is hypothesized to be the etiological agent underlying the patient's condition.

We conducted an analysis of mRNA splicing within the patient and their relatives' blood samples via reverse transcription polymerase chain reaction (RT‐PCR) to assess intronic mRNA splicing. Additionally, we employed a minigene vector construction approach to verify in vitro the splicing of mRNA containing the mutated fragment. Protein structure prediction analysis of the aberrant mRNA was performed using PyMOL software.

The patient harbors a novel mutation in the MBD5 gene: c.114‐13A>G. Analysis of the patient's blood sample revealed the presence of aberrantly sized mRNA molecules. Utilizing a minigene approach, we discovered that this mutation results in the generation of two types of abnormally sized mRNAs. The first type of abnormal splicing leads to a 12‐base pair retention at the 3′ end of intron 6, and the second type of abnormal splicing causes exon 7 skipping.

In accordance with the “Standards and Guidelines for the Interpretation of Sequence Variants” established by the American College of Medical Genetics and Genomics (ACMG), the novel mutation c.114‐13A>G in the MBD5 gene meets the criteria for PS2 (the variant is de novo and not inherited from either parent) and PS3 (the variant affects mRNA splicing, resulting in aberrant transcripts). We propose that the c.114‐13A>G variant, located within intron 6 of the MBD5 gene, is pathogenic. This discovery not only expands the repository of pathogenic variants for MBD5 but also provides additional insights into intronic mutations of the MBD5 gene, thereby offering significant information for the genetic diagnosis of Autosomal Dominant Intellectual Disability Type 1.

The novel intronic potentially pathogenic mutation in the MBD5 gene results in aberrant splicing of mRNA within the body. The protein transcribed from this abnormal mRNA undergoes changes in its spatial structure, with alterations in the electrostatic potential on the protein surface. This newly identified mutation may be the cause of the patient's disease, providing a new pathogenic mutation site for the MBD5 gene in clinical research and expanding the mutation database for the MBD5 gene.

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