Protein details/Single nucleotide variation

The single nucleotide variation section of the Protein details page in GlyGen provides a detailed list of somatic and germline nucleotide mutations.

Single Nucleotide Variation

Single nucleotide variation is presented in 2 tabs on the Protein details page in GlyGen.

This tab shows a list of mutations in the genetic sequence that are associated with a disease. The following columns are presented in the table:

Source - GlyGen evidence linking to the databases and papers that provided the glycosylation information
Filter annotations - Pass/fail filter results from mapping cancer terms to Disease Ontology ID. Eg. Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%)
Genomic locus - The genomic position of the reported mutation. Eg. Chr7:81399287
Start Pos. - Start position of the site in the amino acid sequence. Eg. 1
End Pos. - End position of the site in the amino acid sequence. Eg. 1
Sequence - Reference or wild-type amino acid residue change resulting from variation. Eg. M→ L
Disease - DOID and term corresponding to reported disease. Eg. thyroid gland cancer (DOID:1781)
MAF - The frequency at which the second most common allele occurs in a given population.

This tab shows a list of mutations in the genetic sequence that are not associated with a disease. The following columns are presented in the table:

Source - GlyGen evidence linking to the databases and papers that provided the glycosylation information
Filter annotations -
Genomic locus -
Start Pos. -
End Pos. -
Sequence -
MAF -