PupasView

PupasView prioritizes functionally relevant single nucleotide polymorphisms (SNPs) to support identification of variants that affect splicing, transcription factor binding, and protein function in studies of multifactorial disorders.

Key Features:

• Integration of Functional Information: Retrieves SNPs that may impact conserved regions critical for gene processing, such as intron/exon boundaries and exonic splicing enhancers.
• Prediction of Transcription Factor Binding Sites: Identifies SNPs predicted to disrupt potential transcription factor binding sites that can alter gene regulation and expression.
• Amino Acid Changes and Pathological Effects: Assesses amino acid substitutions within proteins and estimates putative pathological effects to flag variants with possible disease relevance.
• Utilization of Ensembl Mapping: Leverages SNP mapping data from Ensembl to ensure comprehensive genomic coverage and accurate SNP selection.
• Application in Multifactorial Disorders: Focuses on functional SNPs to increase the sensitivity of gene identification efforts for multifactorial disorders.

Scientific Applications:

• Prioritization for Multifactorial Disorders: Prioritizes functionally annotated SNPs to improve the likelihood of identifying genes contributing to multifactorial disorders.
• Studies of Phenotypic Variation and Disease Susceptibility: Supports investigations into the genetic basis of phenotypic variation and susceptibility to disease by providing a refined list of candidate functional variants.

Methodology:

Applies Ensembl SNP mapping and integrated filters on validation status, SNP type, allele frequency/population data, and putative functional properties to produce a refined list of candidate SNPs.