Paralog disease annotation

This query annotates variants with gene symbols, disease phenotypes associated with the gene symbol and paralogs of each gene symbol with the associated disease phenotypes.

Paralog Disease Annotation module in Sequence Miner

Example use case

The user has identified a list of variants in subjects with the same disorder and wishes to list the gene paralogs, along with any corresponding clinical annotation. The genes and gene paralogs will comprise a candidate genelist that could be used in a new study.

Interpreting the output

The output annotates the gene symbol that maps to the genomic coordinates of the input variants. For each gene symbol, disease annotations are added from ClinVar, HGMD, and OMIM. Additionally, the paralogs of the given gene are listed with their corresponding disease annotations.

Column descriptions

Report output columns and descriptions

Group	Column	Description
Basic	Call
	CHROM
	POS
	Reference
gene	diseases	Diseases known to be associated with the gene as annotated by HGMD, ClinVar, and OMIM
	end	The end base pair position of the gene
	par_diseases	The diseases known to be associated with the paralog genes as annotated by HGMD, ClinVar, and OMIM
	paralogs	The paralog genes of the indicated gene symbol as annotated by Ensembl
	start	The start base pair position of the gene (zero based, i.e., the position of the base pair before the first base pair in the gene)
	Symbol	Gene identified by viewing variant in Ensembl; outputs HGNC gene symbol for gene identified (clone name provided when HGNC unavailable)
Other columns	distance	The shortest distance from the variant to the transcript