Description
The TP53 p.Asn239Asp variant was identified in 2 of 474 proband chromosomes (frequency: 0.004) from individuals or families with myelodysplastic syndrome or lung cancer (Belickova 2016, Fouquet 2004). The variant was also identified in dbSNP (ID: rs876660807) as "With Likely pathogenic allele", ClinVar (classified as likely pathogenic by Ambry Genetics and as uncertain significance by Invitae). The variant was not identified in LOVD 3.0 or UMD-LSDB. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The p.Asn239 residue is conserved across mammals and other organisms, and four out of four computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. Functional assays in yeast showed that this variant eliminates the transactivation activity of p53 (Flaman 1998; Jordan 2010). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.
| # | Sample | Method | Observation |
|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences |
|---|
| 1 | unknown | yes | not provided | not provided | not provided | | 1 | not provided | not provided | not provided |
