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A null allele is a mutant copy of a gene at a locus that completely lacks that gene's normal function. This can be the result of the complete absence of the gene product (protein, RNA) at the molecular level, or the expression of a non-functional gene product. At the phenotypic level, a null allele is indistinguishable from a deletion of the entire locus.
A mutant allele that produces no protein is called a protein null (shown by western analysis), and one that produces no RNA is called an RNA null (shown by Northern analysis or by DNA sequencing of a deletion allele). A genetic null or amorphic allele has the same phenotype when homozygous as when heterozygous with a deficiency that disrupts the locus in question. A genetic null allele can be a protein and RNA null, but can also express normal levels of a gene product that is non-functional due to mutation.
Another definition of null allele concerning molecular markers, refers to such a marker in the case it can no longer be detected because of a mutation. For example, microsatellites (i.e. a repetitive sequence of DNA, in which the repeat is rather short) are used as molecular markers amplifying them through PCR. To do so, a primer or oligonucleotide aligns with either of ends of the locus. If a mutation occurs in the annealing site, then the marker can no longer be used and the allele is turned into a null allele.
One example of a null allele is the 'O' blood type allele in the human A, B and O blood type system. The alleles for the A-antigen and B-antigen are co-dominant, thus they are both phenotypically expressed if both are present. The allele for O blood type, however, is a mutated version of the allele for the A-antigen, with a single base pair change due to genetic mutation. The protein coded for by the O allele is enzymatically inactive and therefore the O allele is expressed phenotypically in homozygous OO individuals as the lack of any blood antigen. Thus we may consider the allele for the O blood type as a null allele.