Hi,
Through Sanger sequencing found a missense variant in one of the exons of a gene. That mutation is not found in dbsnp database. How to predict the pathogenicity of that one missense variant?
Two previous answers with more tools:
Posting a an answer in order to link up all of these old threads.
Kevin
In addition to tools like SIFT or Polyphen which you already included in your tags there are other calculations, such as CADD and Fathmm, which integrate lots of information for that position/variant. Another source of evidence is using transcript-expression information. dbSNP is one source, but more valuable would be to look at the frequency of the variant in gnomad.
But at the end of the day, all of these are just predictions and you'll need more genetic or functional evidence to draw any conclusions.
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version 2.3.6
Like your tags already hint, try SIFT or Polyphen.
SIFT (https://sift.bii.a-star.edu.sg/www/SIFT4G_vcf_submit.html) requires a VCF file. So I created a single entry VCF file with the headers.
It din't annotate this entry and returned a empty vcf file.
https://sift.bii.a-star.edu.sg/www/SIFT_seq_submit2.html
Use the amino acid sequence instead.
Thanks Benn for the link for aa sequence. I took the amino acid seq from NCBI protein database and provided the amino acid change at that specific position. It completed successfully. It looks like "deleterious mutation".