Prediction of the damage-associated non-synonymous single nucleotide polymorphisms in the human MC1R gene

PloS One
Diego HeppThales Renato Ochotorena de Freitas

Abstract

The melanocortin 1 receptor (MC1R) is involved in the control of melanogenesis. Polymorphisms in this gene have been associated with variation in skin and hair color and with elevated risk for the development of melanoma. Here we used 11 computational tools based on different approaches to predict the damage-associated non-synonymous single nucleotide polymorphisms (nsSNPs) in the coding region of the human MC1R gene. Among the 92 nsSNPs arranged according to the predictions 62% were classified as damaging in more than five tools. The classification was significantly correlated with the scores of two consensus programs. Alleles associated with the red hair color (RHC) phenotype and with the risk of melanoma were examined. The R variants D84E, R142H, R151C, I155T, R160W and D294H were classified as damaging by the majority of the tools while the r variants V60L, V92M and R163Q have been predicted as neutral in most of the programs The combination of the prediction tools results in 14 nsSNPs indicated as the most damaging mutations in MC1R (L48P, R67W, H70Y, P72L, S83P, R151H, S172I, L206P, T242I, G255R, P256S, C273Y, C289R and R306H); C273Y showed to be highly damaging in SIFT, Polyphen-2, MutPred, PANTHER and PROVEAN scores. Th...Continue Reading

References

Feb 1, 1996·Biochemical Society Transactions·P G Strange
Jul 15, 1999·Biochemical and Biophysical Research Communications·H B SchiöthJ L Rees
Oct 13, 2000·Human Molecular Genetics·N FlanaganJ L Rees
Mar 20, 2001·American Journal of Human Genetics·M T BastiaensUNKNOWN Leiden Skin Cancer Study Team
Feb 8, 2002·American Journal of Human Genetics·Peter A KanetskyTimothy R Rebbeck
Dec 11, 2002·European Journal of Biochemistry·Jesús Sánchez MásCelia Jiménez-Cervantes
Jun 21, 2003·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Michele VendruscoloChristopher M Dobson
Jun 26, 2003·Nucleic Acids Research·Pauline C Ng, Steven Henikoff
Jul 10, 2003·Annals of the New York Academy of Sciences·R A SturmN G Martin
Sep 4, 2003·Genome Research·Paul D ThomasApurva Narechania
Nov 18, 2003·Annual Review of Genetics·Jonathan L Rees
Jan 8, 2004·Human Molecular Genetics·David L DuffyRichard A Sturm
Oct 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Paul D Thomas, Anish Kejariwal
Feb 18, 2005·Drug Metabolism and Disposition : the Biological Fate of Chemicals·Hiroyuki HichiyaJun-ichi Sawada
Jan 18, 2006·Journal of Molecular Biology·Peng Yue, John Moult
Mar 23, 2006·BMC Bioinformatics·Peng YueJohn Moult
Jul 11, 2006·Annual Review of Genomics and Human Genetics·Pauline C Ng, Steven Henikoff
May 29, 2007·Nucleic Acids Research·Yana Bromberg, Burkhard Rost
Jul 10, 2007·Human Molecular Genetics·Kimberley A BeaumontRichard A Sturm
Aug 28, 2007·Genomics·R RajasekaranRao Sethumadhavan
Aug 30, 2007·BMC Genetics·Robert J Klein
Oct 24, 2007·Nature Genetics·Patrick SulemKari Stefansson
Mar 28, 2008·International Journal of Cancer. Journal International Du Cancer·Sara RaimondiMaria Concetta Fargnoli
Apr 18, 2008·BMC Bioinformatics·Emidio CapriottiRita Casadio
Jun 1, 2007·Forensic Science International. Genetics·Gillian Tully
Jul 7, 2009·Nature Genetics·D Timothy BishopJulia A Newton Bishop
Jul 9, 2009·International Journal of Cancer. Journal International Du Cancer·Dominique SchererRajiv Kumar
Aug 12, 2009·Archives of Biochemistry and Biophysics·P David JosephyBengt Mannervik
Apr 1, 2010·Nature Methods·Ivan A AdzhubeiShamil R Sunyaev
Jun 4, 2010·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Ana Luisa KadekaroZalfa A Abdel-Malek

❮ Previous
Next ❯

Citations

Sep 30, 2016·Journal of Biomolecular Structure & Dynamics·Peng SangZhao-Hui Meng
Dec 9, 2016·Pigment Cell & Melanoma Research·Eduardo NagoreRajiv Kumar
Jul 31, 2019·Animal Genetics·Marie Abitbol, Vincent Gache
Jan 23, 2016·The British Journal of Dermatology·C MüllerI Okamoto
Jun 27, 2019·Journal of Cellular Biochemistry·Saranya Gandhi Muruganandhan, Rameshpathy Manian

❮ Previous
Next ❯

Methods Mentioned

BETA
Phenotyping

Software Mentioned

PON
SIFT Tolerant
PROVEAN ( Protein Variation Effect Analyzer )
PhD
SNPs3D
Mutation Assessor
Polyphen
PANTHER ( Protein ANalysis Evolutionary Relationships
MutPred
PROVEAN

Related Concepts

Related Feeds

ALS: Genetics

Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disorder characterized by muscle weakness. ALS is a genetically heterogeneous disorder with several causative genes. Here are the latest discoveries pertaining to the genetics of this disease.

Cardiomyopathy

Cardiomyopathy is a disease of the heart muscle, that can lead to muscular or electrical dysfunction of the heart. It is often an irreversible disease that is associated with a poor prognosis. There are different causes and classifications of cardiomyopathies. Here are the latest discoveries pertaining to this disease.

Amyloid Lateral Sclerosis

Amyotrophic Lateral Sclerosis (ALS) is a progressive nervous system disease associated with the death of neurons that control voluntary muscles. Discover the latest research on ALS here.

ALS: Phenotypes

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disorder characterized phenotypically by progressive muscle weakness. Clinical phenotypes of ALS can be classified based on the pattern, level, and area of onset (e.g. bulbar, cervical, lumbar). Here is the latest research investigating phenotypes of ALS.

ALS: Genetics

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterized by muscle weakness. Here is the latest research investigating genetic alterations in this genetically heterogeneous disorder.

Related Papers

British Journal of Cancer
N HearleR S Houlston
Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology
Peter A KanetskyTimothy R Rebbeck
© 2021 Meta ULC. All rights reserved