In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract

BMC Molecular and Cell Biology
Mingzhou ZhangXuemin Li

Abstract

Gap junction protein alpha 3 (GJA3), an important pathogenic gene of congenital cataracts, encodes the transmembrane protein connexin46, which functions as an intercellular channel for voltage and chemical gating by forming dodecamers. This study systematically collected nsSNP information for the GJA3 gene from SNP databases and literature and screened for nsSNPs with high risks of pathogenicity. A total of 379 nsSNPs of GJA3 were identified. A total of 88 high-risk pathogenic GJA3 nsSNPs were found, including 31 published nsSNPs associated with congenital cataracts and 57 novel nsSNPs predicted by all eight online tools. The 88 high-risk pathogenic mutations, which are related to 67 amino acids in the wild-type sequences, cause a decrease in protein stability according to I-Mutant 3.0, MUpro and INPS. G2 and R33 were predicted to participate in post-translational modification and ligand binding by ModPred, RaptorX Binding and COACH. Additionally, high-risk mutations were likely to involve highly conserved sites, random coils, alpha helixes, and extracellular loops and were accompanied by changes in amino acid size, charge, hydrophobicity and spatial structure. Eighty-eight high-risk pathogenic nsSNPs of GJA3 were screened out ...Continue Reading

References

Oct 1, 1975·International Journal of Radiation Oncology, Biology, Physics·C G Moertel
Dec 1, 1987·Protein Engineering·M Vihinen
Feb 6, 1996·Proceedings of the National Academy of Sciences of the United States of America·J X Jiang, D A Goodenough
Jan 5, 1999·Genome Research·F S CollinsA Chakravarti
Apr 17, 1999·American Journal of Human Genetics·D MackayS Bhattacharya
Sep 8, 1999·Human Mutation·P BrossN Gregersen
Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Jun 8, 2001·The Journal of Biological Chemistry·A BaruchM Bogyo
Jan 29, 2002·Journal of Molecular Biology·Carles Ferrer-CostaXavier de la Cruz
Dec 15, 2004·Biophysical Journal·Miduturu SrinivasVytas K Verselis
Jan 29, 2005·American Journal of Physiology. Cell Physiology·Camillo Peracchia, Lillian L Peracchia
Jun 28, 2005·Nucleic Acids Research·Emidio CapriottiRita Casadio
Jul 19, 2008·Neuron Glia Biology·Eliana ScemesDavid C Spray
Oct 9, 2009·Nature·Teri A ManolioPeter M Visscher
Jan 21, 2010·Physiological Reviews·Richard T MathiasXiaohua Gong
Apr 1, 2010·Nature Methods·Ivan A AdzhubeiShamil R Sunyaev
Dec 15, 2010·Nucleic Acids Research·Laura M BondL James Maher
Jun 13, 2012·Nucleic Acids Research·Ngak-Leng SimPauline C Ng
Jul 21, 2012·Nature Protocols·Morten KällbergJinbo Xu
Oct 12, 2012·PloS One·Yongwook ChoiAgnes P Chan
Jan 18, 2014·FEBS Letters·Viviana M BerthoudEric C Beyer
Apr 1, 2014·Nature Methods·Jana Marie SchwarzDominik Seelow
Jun 4, 2014·Protein Science : a Publication of the Protein Society·Vikas PejaverPredrag Radivojac
Oct 9, 2014·The Journal of Biological Chemistry·Nefeli SlaviMiduturu Srinivas
Feb 7, 2015·Current Opinion in Structural Biology·Tugba G KucukkalEmil Alexov
Nov 19, 2015·Protein Science : a Publication of the Protein Society·Hafumi NishiKengo Kinoshita
May 7, 2016·Bioinformatics·Castrense SavojardoRita Casadio
Apr 30, 2017·Nucleic Acids Research·Víctor López-FerrandoJosep Ll Gelpí
Nov 23, 2017·Nucleic Acids Research·Melissa J LandrumDonna R Maglott
Jul 31, 2018·Nucleic Acids Research·Jinchen LiZhongsheng Sun
Dec 14, 2018·Nature·Janette B MyersSteve L Reichow

❮ Previous
Next ❯

Methods Mentioned

BETA
exome sequencing
acetylation
protein folding

Software Mentioned

PolyPhen
Pmut
TMpred
SOPMA
Mutant
SITE
Polyphen2
PSEP
SIFT
TM

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.