how can I solve a problem in applying a mutation on protein sequence?

Question

[Atefeh]

Hello everyone

I am working with VCF files. I want to extract peptides from mutations that have occurred. for example I have one mutation p.I2447_I2448del and three NM accessions for that in refseq column (NM_015046.7;NM_001351528.2;NM_001351527.1) . I get protein sequence by those accession numbers. now I have three protein sequence and I apply this mutation p.I2447_I2448del for all of them, but in 2447_2448 positions there are SP amino acids instead of II in second protein sequence from NM_001351528.2. So what should I do?

Thanks a lot

[barslmn]

You have RNA accession ids for a protein change. What is the NP accession? Could you check your naming here: https://mutalyzer.nl/ ? Also, HGVS uses three letter amino acid instead of single ones.

[Atefeh]

Thanks for your response. Actually i am using MAF file (other type of vcf file). there is not NP accession number in it. I meant HGVSp_Short.

[cmdcolin]

what did you use to map the VCF to the hgvs?

Answer 1

[Ram]

The three transcripts seem to be from the SETX gene, of which the canonical transcript ID is the first one: NM_015046.7, which translates to the protein NP_055861.3, which has II at positions 2447-2448. You are looking at a different protein product, which is why the co-ordinates don't match. Always look at the protein product from the MANE/canonical transcript first.

[Atefeh]

Thank you so much.

[Ram]

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