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.