Methods and kits are provided for determining which single nucleotide
polymorphism ("SNP") variant of an allele of a heterozygous patient is on
the same mRNA transcript as a disease-causing mutation that is at a
remote region of the gene's mRNA comprising a) an allele-specific reverse
transcription reaction using an allele-specific primer, and b) analysis
of the resulting cDNA product from the reverse transcription reaction at
the region of the mutation to determine the presence or absence of the
mutation on this allele-specific cDNA product.