根据dbSNP的ID来转换成HGVS突变表示形式

ulwvfje — Sun, 10 Apr 2016 01:11:47 +0000

dbSNP的ID直接在NCBI的dbSNP官网可以看到详细介绍，现在已经更新到146版本了，一般人看到一个ID肯定什么信息都获取不到，毕竟这只是人家NCBI规定的一个ID而已。但是HGVS突变形式就有非常详细的信息了。

人类基因组变异协会（HGVS）官方组织规定了mutation该如何记录：http://www.hgvs.org/mutnomen/recs.html 推荐大家都仔细阅读！！！

还有一个程序是根据染色体坐标来得到HGVS突变形式：https://github.com/counsyl/hgvs 这个有点复杂，我们先不讲！

其实YouTube上面有视频教程(BioMart: Variation IDs to HGNC Symbols)，考虑到大部分都无法翻墙，我这里给出一个取巧的解决办法！

取巧的办法就是，根据RS ID号直接组合域名，一下三种方式均可！

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs1800234

http://www.ncbi.nlm.nih.gov/snp/1800234

http://browser.1000genomes.org/Homo_sapiens/Variation/Explore?v=rs1800234

下面详细讲解三种方式的返回结果：

直接爬取dbSNP的返回数据，提取对应的：

比如：http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs1800234

很明显就能看到：

HGVS Names
NC_000022.10:g.46615880T>C NC_000022.11:g.46219983T>C NG_012204.1:g.74382T>C NM_001001928.2:c.680T>C NM_005036.4:c.680T>C NP_001001928.1:p.Val227Ala NP_005027.2:p.Val227Ala XM_005261653.1:c.680T>C XM_005261654.1:c.680T>C XM_005261655.1:c.680T>C

你只需要根据你自己想搜索的ID号来组合一个url

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs197278

等等~~~~~~~~~~

或者直接在NCBI的snp页面根据ID来搜索：

http://www.ncbi.nlm.nih.gov/snp/1800234

AACATGAACAAGGTCAAAGCCCGGG[A/C/T]CATCCTCTCAGGAAAGGCCAGTAAC

Chromosome:: 22:46219983
Gene:: PPARA (GeneView)
Functional Consequence:: intron variant,missense
Validated:: by 1000G,by cluster,by frequency
Global MAF:: C=0.0170/85
HGVS:: NC_000022.10:g.46615880T>C, NC_000022.11:g.46219983T>C, NG_012204.1:g.74382T>C, NM_001001928.2:c.680T>C, NM_005036.4:c.680T>C, NP_001001928.1:p.Val227Ala, NP_005027.2:p.Val227Ala, XM_005261653.1:c.680T>C, XM_005261654.1:c.680T>C, XM_005261655.1:c.680T>C, XM_005261655.2:c.680T>C, XM_005261656.1:c.680T>C, XM_005261656.2:c.680T>C, XM_005261657.1:c.680T>C, XM_005261658.1:c.680T>C, XM_006724269.2:c.680T>C, XM_006724270.2:c.680T>C, XM_011530239.1:c.680T>C, XM_011530240.1:c.680T>C, XM_011530241.1:c.680T>C, XM_011530242.1:c.680T>C, XM_011530243.1:c.680T>C, XM_011530244.1:c.278T>C, XM_011530245.1:c.278T>C, XP_005261710.1:p.Val227Ala, XP_005261711.1:p.Val227Ala, XP_005261712.1:p.Val227Ala, XP_005261713.1:p.Val227Ala, XP_005261714.1:p.Val227Ala, XP_005261715.1:p.Val227Ala, XP_006724332.1:p.Val227Ala, XP_006724333.1:p.Val227Ala, XP_011528541.1:p.Val227Ala, XP_011528542.1:p.Val227Ala, XP_011528543.1:p.Val227Ala, XP_011528544.1:p.Val227Ala, XP_011528545.1:p.Val227Ala, XP_011528546.1:p.Val93Ala, XP_011528547.1:p.Val93Ala, XR_244379.1:n.735+1578T>C, XR_937869.1:n.827+1578T>C, XR_937870.1:n.822+1582T>C

PubMed Protein3D

还有很多其它类似的数据库都提供类似的服务：

比如Ensembl提供的千人基因组计划的接口：

http://browser.1000genomes.org/Homo_sapiens/Variation/Explore?v=rs1800234

This variation has 11 HGVS names - click the plus to show

22:g.46615880T>C
ENST00000493286.1:n.890T>C
ENST00000262735.5:c.680T>C
ENSP00000262735.5:p.Val227Ala
ENST00000396000.2:c.680T>C
ENSP00000379322.2:p.Val227Ala
ENST00000434345.2:c.508+1582T>C
ENST00000407236.1:c.680T>C
ENSP00000385523.1:p.Val227Ala
ENST00000402126.1:c.680T>C
ENSP00000385246.1:p.Val227Ala

生信菜鸟团 » HGVS

根据dbSNP的ID来转换成HGVS突变表示形式