Mutation database for protein

Question

[ashamscsoft]

I need one help can somebody help me? I need to know is there any database available for protein mutation information like HGMD is available? I saw protein mutant database(PMD) but im unable to get into that page. Could someone help me?

[WouterDeCoster]

Can you be more specific about what you need?

Answer 1

[Ram]

All protein mutations have underlying DNA/RNA mutations.

HGMD has a Missense/Nonsense section for each gene that shows you protein changes. You might also have to look through insertions, deletions and indels to find in-frame variants that lead to a protein change, or frameshift variants (if you're looking for such) as well.

For the insertions/deletions/indels, you will have to use the python hgvs module to translate cDNA changes to predicted protein changes.

[ashamscsoft]

ya i know about HGMD, but there is no separate database for protein mutation?

[WouterDeCoster]

What is a protein mutation exactly? Mutations in protein coding sequences? Mutations changing protein coding sequences?

[ashamscsoft]

Both will be same when, what ram is true if the protein mutations underlie DNA/RNA. Both will be different when there is no mutation in DNA/RNA, and the mutation occurs in protein due to misfold etc.

[WouterDeCoster]

Are you sure you know what you're talking about? (Or perhaps I misunderstand)

[ashamscsoft]

k now i got a doubt can u clear my doubt without mutation in DNA/RNA, is there a chance of a mutation in a protein?

[WouterDeCoster]

Cystic fibrosis most certainly occurs due to a genetic mutation (potentially resulting in protein misfolding). In addition, there is no such a thing as a non-genetic mutation. Every mutation is "genetic".

[ashamscsoft]

Ya im sorry ur right but my doubt is without mutation in DNA/RNA, is there a chance of a mutation in a protein?

[ashamscsoft]

i think protein mutation is Mutations changing protein coding sequences. Am i rite

[WouterDeCoster]

I haven't heard of the term "protein mutation".

[Ram]

Most variants affect the DNA sequence. If you are looking for aberrations brought in during post translational modifications, such as misfolding, they are highly specific to where they happen and are quite rare. I doubt there is a database out there for all proteins.

You may have to focus on your proteins of interest and build one for yourself probably based on molecular dynamics and sequence analysis.

[WouterDeCoster]

Theoretically yes, you can have differences in a protein without mutation in the DNA, because RNA editing enzymes exist which could posttranslationally modify a transcript, resulting in a different codon, resulting in a different protein. But that's probably not a frequent event.