Abstract: The technology disclosed relates to a variant pathogenicity classifier. The variant pathogenicity classifier comprises memory and runtime logic. The memory stores (i) a reference amino acid sequence of a protein, (ii) an alternative amino acid sequence of the protein that contains a variant amino acid caused by a variant nucleotide, and (iii) a protein contact map of the protein. The runtime logic has access to the memory, and is configured to provide (i) the reference amino acid sequence, (ii) the alternative amino acid sequence, and (iii) the protein contact map as input to a first neural network, and to cause the first neural network to generate a pathogenicity indication of the variant amino acid as output in response to processing (i) the reference amino acid sequence, (ii) the alternative amino acid sequence, and (iii) the protein contact map.

Abstract: The technology disclosed relates to a variant pathogenicity prediction network. The variant pathogenicity classifier includes memory, a variant encoding sub-network, a protein contact map generation sub-network, and a pathogenicity scoring sub-network. The memory stores a reference amino acid sequence of a protein, and an alternative amino acid sequence of the protein that contains a variant amino acid caused by a variant nucleotide. The variant encoding sub-network is configured to process the alternative amino acid sequence, and generate a processed representation of the alternative amino acid sequence. The protein contact map generation sub-network is configured to process the reference amino acid sequence and the processed representation of the alternative amino acid sequence, and generate a protein contact map of the protein. The pathogenicity scoring sub-network is configured to process the protein contact map, and generate a pathogenicity indication of the variant amino acid.