SNP analysis of follistatin gene associated with polycystic ovarian syndrome

Follistatin has been reported as a candidate gene for polycystic ovarian syndrome (PCOS) based on linkage and association studies. In this study, investigation of polymorphisms in the FST gene was done to determine if genetic variation is associated with susceptibility to PCOS. The nucleotide sequen...

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Main Authors:	Panneerselvam, Palanisamy, Sivakumari, Kanakarajan, Jayaprakash, Ponmani, Srikanth, Ramanathan
Format:	Online
Language:	English
Published:	Dove Medical Press 2010
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170008/

id	pubmed-3170008
recordtype	oai_dc
spelling	pubmed-31700082011-09-14 SNP analysis of follistatin gene associated with polycystic ovarian syndrome Panneerselvam, Palanisamy Sivakumari, Kanakarajan Jayaprakash, Ponmani Srikanth, Ramanathan Original Research Follistatin has been reported as a candidate gene for polycystic ovarian syndrome (PCOS) based on linkage and association studies. In this study, investigation of polymorphisms in the FST gene was done to determine if genetic variation is associated with susceptibility to PCOS. The nucleotide sequence of human follistatin and the protein sequence of human follistatin were retrieved from the NCBI database using Entrez. The follistatin protein of human was retrieved from the Swiss-Prot database. There are 344 amino acids and the molecular weight is 38,007 Da. The ProtParam analysis shows that the isoelectric point is 5.53 and the aliphatic index is 61.25. The hydropathicity is −0.490. The domains in FST protein are as follows: Pfam-B 5005 domain from 1 to 92; EGF-like subdomain from 93 to 116; Kazal 1 domain, occurred in three places, namely, 118–164, 192–239, and 270–316. There are 31 single-nucleotide polymorphisms (SNPs) for this gene. Some are nonsynonymous, some occur in the intron region, and some in an untranslated region. Two nonsynonymous SNPs, namely, rs11745088 and rs1127760, were taken for analysis. In the SNP rs11745088, the change is E152Q. Likewise, in rs1127760, the change is C239S. SIFT (Sorting Intolerant from Tolerant) showed positions of amino acids and the single letter code of amino acids that can be tolerated or deleterious for each position. There were six SNP results and each result had links to it. The dbSNP id, primary database id, and the type of mutation whether silent and if occurring in coding region are given as phenotype alterations. The FASTA format of protein was given to the nsSNP Analyzer tool, and the variation E152Q and C239S were given as inputs in the SNP data field. E152Q change was neutral and C239S causes disease. Using PANTHER for evolutionary analysis of coding SNPs, the protein sequence was given as input and analyzed for the E152Q and C239S SNPs for deleterious effect on protein function. The genetic association database results showed that FST gene SNPs are linked to PCOS coming under the disease class of metabolic disorders. The list of intronic and synonymous SNPs, with their nucleotide position, amino acid change information, and dbSNP link, is provided for further analysis. Dove Medical Press 2010-12-13 /pmc/articles/PMC3170008/ /pubmed/21918632 http://dx.doi.org/10.2147/AABC.S11013 Text en © 2010 Panneerselvam et al, publisher and licensee Dove Medical Press Ltd. This is an Open Access article which permits unrestricted noncommercial use, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Panneerselvam, Palanisamy Sivakumari, Kanakarajan Jayaprakash, Ponmani Srikanth, Ramanathan
spellingShingle	Panneerselvam, Palanisamy Sivakumari, Kanakarajan Jayaprakash, Ponmani Srikanth, Ramanathan SNP analysis of follistatin gene associated with polycystic ovarian syndrome
author_facet	Panneerselvam, Palanisamy Sivakumari, Kanakarajan Jayaprakash, Ponmani Srikanth, Ramanathan
author_sort	Panneerselvam, Palanisamy
title	SNP analysis of follistatin gene associated with polycystic ovarian syndrome
title_short	SNP analysis of follistatin gene associated with polycystic ovarian syndrome
title_full	SNP analysis of follistatin gene associated with polycystic ovarian syndrome
title_fullStr	SNP analysis of follistatin gene associated with polycystic ovarian syndrome
title_full_unstemmed	SNP analysis of follistatin gene associated with polycystic ovarian syndrome
title_sort	snp analysis of follistatin gene associated with polycystic ovarian syndrome
description	Follistatin has been reported as a candidate gene for polycystic ovarian syndrome (PCOS) based on linkage and association studies. In this study, investigation of polymorphisms in the FST gene was done to determine if genetic variation is associated with susceptibility to PCOS. The nucleotide sequence of human follistatin and the protein sequence of human follistatin were retrieved from the NCBI database using Entrez. The follistatin protein of human was retrieved from the Swiss-Prot database. There are 344 amino acids and the molecular weight is 38,007 Da. The ProtParam analysis shows that the isoelectric point is 5.53 and the aliphatic index is 61.25. The hydropathicity is −0.490. The domains in FST protein are as follows: Pfam-B 5005 domain from 1 to 92; EGF-like subdomain from 93 to 116; Kazal 1 domain, occurred in three places, namely, 118–164, 192–239, and 270–316. There are 31 single-nucleotide polymorphisms (SNPs) for this gene. Some are nonsynonymous, some occur in the intron region, and some in an untranslated region. Two nonsynonymous SNPs, namely, rs11745088 and rs1127760, were taken for analysis. In the SNP rs11745088, the change is E152Q. Likewise, in rs1127760, the change is C239S. SIFT (Sorting Intolerant from Tolerant) showed positions of amino acids and the single letter code of amino acids that can be tolerated or deleterious for each position. There were six SNP results and each result had links to it. The dbSNP id, primary database id, and the type of mutation whether silent and if occurring in coding region are given as phenotype alterations. The FASTA format of protein was given to the nsSNP Analyzer tool, and the variation E152Q and C239S were given as inputs in the SNP data field. E152Q change was neutral and C239S causes disease. Using PANTHER for evolutionary analysis of coding SNPs, the protein sequence was given as input and analyzed for the E152Q and C239S SNPs for deleterious effect on protein function. The genetic association database results showed that FST gene SNPs are linked to PCOS coming under the disease class of metabolic disorders. The list of intronic and synonymous SNPs, with their nucleotide position, amino acid change information, and dbSNP link, is provided for further analysis.
publisher	Dove Medical Press
publishDate	2010
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170008/
_version_	1611474674150014976

SNP analysis of follistatin gene associated with polycystic ovarian syndrome

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