Methods and kits are provided for determining which single nucleotide polymorphism (“SNP”) variant of an allele of a heterozygous patient is on the same allele 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 which recognizes one SNP variant, wherein further the 3′ end of the primer is positioned at the SNP nucleotide position, 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, wherein the allele specific primer is shorter than about 20 nucleotides.