H1407Y could be any one of hundreds of genes but if you know the name of the gene that you are working on go to dbsnp at https://www.ncbi.nlm.nih.gov/snp/

and put the name of the gene into search box and it will give you the co ordinates of all of the snps in that gene. Match your change with the dbsnp change that matches base change and position

Hi Aoife H. , Hi Paul Rutland

genomic coordinates, gene name and number of AA doesn't mean nothing when missing the first information, the genome build number (and maybe too the number of the transcrit when more than one exists). since there is a shift between all assemblies, just precise the gene and position, and we could help you, by use of the NCBI or UCSC genome browsers.

all the best

fred

Thank you for the replies, Paul Rutland and Frederic Lepretre .

The variant I am trying to characterize is PIK3CA H1407Y, however the NCBI website is showing no results for that variant in that gene.

try the UCSC genome browser. there are a lot of optional tracks to see variations, but maybe your variant is new and has not been yet described in databases...

fred

I thought you could try ensemble which shows changes in genomic and cdna sequences for example

http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000121879;r=3:179148114-179240093;t=ENST00000263967

but I could not find a transcript long enough to have a H1407y change in it but you may want to have a look with your better knowledge of the gene and its variants.

Thank you for all the help, Paul Rutland and Frederic Lepretre .

For me to find the exact base pair position of the SNP within the gene coordinate range : 179,148,114 to 179,240,093 The SNP occurs on the nucleotide bp @ position 3140. Do I just add 3140 to the starting range of the gene?

I tried that with another well known gene and it didn't give me the correct nucleotide where the SNP occurs.

Thanks so much, I really appreciate it!

Hi Aoife,

The coding nomenclature should be described using the “A” of the ATG translation initiation codon as position number 1. I attach a definitive nomenclature paper for your interest.

in attach the genomic positions as Aoife asked, but no informations on SNP in this species.

fred

Hi Aoife,

PIK3CA H1407Y is not available as there is no such transcript with aa length greater than 1068 aa. You can check on Ensembl, link is as follows:

https://asia.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000121879;r=3:179148114-179240093

Furthermore, you can find the exact genomic position and position in the gene from NCBI dbSNP and Varsome.

https://varsome.com/

Mehran Akhtar well that makes so much more sense on why I couldn't find it. It turned out to be a typing error on the data that was given to me.

Thank you for all your help, I've really learned a lot from your advice.

PIK3CA is not MC4R, is there a mistake?

Frederic Lepretre yes Frederic, there was a typing error on the PIK3CA variant number, hence the confusion in finding it.