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Clinical, Functional and Fitness Consequences of Genetic Variants
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Clinical, Functional and Fitness Consequences of Genetic Variants

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (20 April 2024) | Viewed by 1321

Special Issue Editor

Dr. Panagiotis Katsonis

E-Mail Website
Guest Editor
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Interests: genome interpretation; protein coding variants; pathogenic effects; disease driver genes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A major bottleneck in interpreting genetic data is estimating the impact of each single variant. Genome-wide association studies (GWASs) and family segregation studies (FSSs) may associate diseases with single variants or with genes. Experimental studies may associate variants with the loss or gain of protein function and indicate alterations in specific biological processes. Computational studies may use evolutionary and structural information to suggest variant effects on fitness and mechanistic insights, respectively. These studies improve our understanding of variant consequences and help in interpreting variants that are currently described as variants of unknown significance (VUS).

In this Special Issue, we welcome the submission of reviews, original articles, and short reports that cover any aspects of variant consequences. These may include works focused on specific genes, biological functions, phenotypes, or samples.

Dr. Panagiotis Katsonis
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genome interpretation
  • protein function
  • fitness effect
  • variant impact
  • trait association
  • driver mutation
  • human genome
  • gene pathway
  • machine learning

Published Papers (1 paper)

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Research

13 pages, 1758 KiB  
Article
Novel Variants of PPP2R1A in Catalytic Subunit Binding Domain and Genotype–Phenotype Analysis in Neurodevelopmentally Delayed Patients
by Yanyan Qian, Yinmo Jiang, Ji Wang, Gang Li, Bingbing Wu, Yuanfeng Zhou, Xiu Xu and Huijun Wang
Genes 2023, 14(9), 1750; https://doi.org/10.3390/genes14091750 - 01 Sep 2023
Viewed by 1008
Abstract
Neurodevelopmental disorders (NDDs) are a group of high-incidence rare diseases with genetic heterogeneity. PPP2R1A, the regulatory subunit of protein phosphatase 2A, is a recently discovered gene associated with NDDs. Whole/clinical exome sequencing was performed in five patients with a family with NDDs. In [...] Read more.
Neurodevelopmental disorders (NDDs) are a group of high-incidence rare diseases with genetic heterogeneity. PPP2R1A, the regulatory subunit of protein phosphatase 2A, is a recently discovered gene associated with NDDs. Whole/clinical exome sequencing was performed in five patients with a family with NDDs. In vitro experiments were performed to evaluate the mutants’ expression and interactions with the complex. The genotype–phenotype correlations of reported cases as well as our patients with PPP2R1A variants were reviewed. We reported five unrelated individuals with PPP2R1A variants, including two novel missense variants and one frameshift variant. The protein expression of the Arg498Leu variant was less than that of the wild-type protein, the frameshift variant Asn282Argfs*14 was not decreased but truncated, and these two variants impaired the interactions with endogenous PPP25RD and PPP2CA. Furthermore, we found that pathogenic variants clustered in HEAT repeats V, VI and VII, and patients with the Met180Val/Thr variants had macrocephaly, severe ID and hypotonia, but no epilepsy, whereas those with Arg258 amino acid changes had microcephaly, while a few had epilepsy or feeding problems. In this study, we reported five NDD patients with PPP2R1A gene variants and expanded PPP2R1A pathogenic variant spectrum. The genotype and phenotype association findings provide reminders regarding the prognostication and evidence for genetic counseling. Full article
(This article belongs to the Special Issue Clinical, Functional and Fitness Consequences of Genetic Variants)
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