SNPs name (protein change)

Question

[fatma.mokhtar]

Hi all,

I have different SNPs, most of them are in intron variants. I would like to find out the SNP name. For instance, the SNP rs4148217 in ABCG8 has this name: T400K, which indicates the protein change. I would like to find a program that can give me the (protein change name). I have checked my SNPs in ClincVar, and I was unable to find it, could you please advise me on a helpful program?

Thank you in advance, Fatma

[Hamid Ghaedi]

EDIT: @Pierrre answered your question. I have assumed you have a list of common name for SNPs and want to retrieve rs#.

Having had a similar problem-Having a list of variants in non-standard format and wanna have relevant rs#- a couple of years ago I went through it by using Variant Name Mapper and SNPedia.

for Variant Name Mapper : you can insert your variant name/gene name in the search box (Should do manually :((). It will return you a table including rs# for the variant. For example the result for MTHFR gene is https://phgkb.cdc.gov/PHGKB/mapperSummary.action?query=MTHFR&Mysubmit=Search . As you can see there is the common name and relevant rs#.

However, SNPedia is one of the references used by the Variant Name Mapper, it worth to query this website by yourself also.

More common an SNP, the more chance to find relevant rs# using this method.

Answer 1

[Pierre Lindenbaum]

paste your rs# in ensembl VEP: https://www.ensembl.org/Multi/Tools/VEP?db=core

ABCG8: ENST00000272286

Type: protein_coding missense_variant

Amino acids: T/K

SIFT: tolerated

PolyPhen: benign

Answer 2

[agorelick]

I would go for Variant Effect Predictor (VEP) as Pierre Lindenbaum said.

If you only need to do this a few times, you can submit a list of RS IDs to the VEP web interface (https://uswest.ensembl.org/info/docs/tools/vep/online/index.html) and it will annotate each one. There are many optional annotations, but if you want protein change annotations, enable the Biotype, HGVS and Protein options, these should give you residue and amino acid change information for the protein-coding variants. Then just filter the results Biotype=='protein_coding'.

If you need to do this many times, then you can install VEP on a server, but I've heard it's a pain to install (it requires downloading large databases for VEP to access to generate its various annotations).