Differential Domain Distribution of gnomAD- and Disease-Linked Connexin Missense Variants

Abstract

Twenty-one human genes encode connexins, a family of homologous proteins making gap junction (GJ) channels, which mediate direct intercellular communication to synchronize tissue/organ activities. Genetic variants in more than half of the connexin genes are associated with dozens of different Mendelian inherited diseases. With rapid advances in DNA sequencing technology, more variants are being identified not only in families and individuals with diseases but also in people in the general population without any apparent linkage to Mendelian inherited diseases. Nevertheless, it remains challenging to classify the pathogenicity of a newly identified connexin variant. Here, we analyzed the disease- and Genome Aggregation Database (gnomAD, as a proxy of the general population)-linked variants in the coding region of the four disease-linked α connexin genes. We found that the most abundant and position-sensitive missense variants showed distinct domain distribution preference between disease- and gnomAD-linked variants. Plotting missense variants on topological and structural models revealed that disease-linked missense variants are highly enriched on the structurally stable/resolved domains, especially the pore-lining domains, while the gnomAD-linked missense variants are highly enriched in the structurally unstable/unresolved domains, especially the carboxyl terminus. In addition, disease-linked variants tend to be on highly conserved residues and those positions show evolutionary co-variation, while the gnomAD-linked missense variants are likely on less conserved residue positions and on positions without co-variation. Collectively, the revealed distribution patterns of disease- and gnomAD-linked missense variants further our understanding of the GJ structure–biological function relationship, which is valuable for classifying the pathogenicity of newly identified connexin variants.

Missense Variants Reveal Functional Insights Into the Human ARID Family of Gene Regulators

“…While calculating variant distributions along protein sequences can help to identify essential domains, it fails to consider the arrangement of variants in 3D space. 6 This has been addressed by manual mapping of variants 11 or computational mapping of variant depletion scores directly onto protein structures. For example, Hicks et al, developed a ‘3D Tolerance Score’ which compares an observed and expected number of missense variants in 5 Å-radius spheres around individual atoms in a 3D structure.…”

The Hydrophobic Residues in Amino Terminal Domains of Cx46 and Cx50 Are Important for Their Gap Junction Channel Ion Permeation and Gating

“…Second, hydrophobic residues are highly conserved in Cx46 and Cx50 as well as among α and other families of connexins, and the equivalent hydrophobic residue positions are almost all able to form amphipathic α-helix to likely interact with their TM1/2 domains. These hydrophobic residue positions are also frequently found to be hot spots for inherited disease-linked connexin mutants, such as oculodentodigital dysplasia-linked mutants in another α-connexin Cx43 (L7, L11) [ 44 ] and CMT1X-linked mutants in a β-connexin Cx32 on equivalent positions (W3, L9, L10) [ 37 ]. Functional studies on mutations of the hydrophobic NT residues of Cx32, including W3D, L6D, L9D, and L10D all resulted in non-functional GJs [ 17 ].…”

Evaluating gap junction variants for a role in pediatric cataract: an overview of the genetic landscape and clinical classification of variants in the GJA3 and GJA8 genes

“…This was hampered by a lack of strong functional evidence evaluating the role of various domains in gap junction or hemichannel function. Ultimately, it was applied using data regarding the location of known disease-causing variants collated and assessed by Bai et al [143], which may result in circular arguments regarding the classification of variants in these regions that were used to define these regions. This is a limitation of the current approach and should be addressed for more accurate classifications in the future.…”