ClinVar Genomic variation as it relates to human health

The NM_000546.6:c.993+1del is a deletion of a single G nucleotide within the canonical donor site of exon 9 of TP53. Through exon 9 skipping, the variant is observed in an RT-PCR assay to produce multiple aberrant transcripts encoding frameshift alterations predicted to induce nonsense-mediated decay (PVS1(RNA); PMID: 10980596). This variant has been reported in 1 proband meeting Classic LFS criteria. Based on this evidence, this variant scores 1 total points meeting the TP53 VCEP phenotype scoring criteria of 1-1.5 points. (PS4_Supporting; PMID: 10980596). This variant has been reported to segregate with LFS-associated cancers in 3-4 meioses in 1 family (PP1; PMID: 10980596). This variant is absent from gnomAD v4.1.0 (PM2_Supporting).. In summary, this variant meets criteria to be classified as likely pathogenic for Li-Fraumeni syndrome based on the ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: PVS1(RNA), PS4_Supporting, PP1, PM2_Supporting (Bayesian Points: 7; VCEP specifications version 2.0; 7/24/2024).

Variant summary: TP53 c.993+1delG is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: four predict the variant abolishes a 5' splicing donor site. These predictions were confirmed by a publication that demonstrated exon 9 skipping in a patient derived immortalized cell line, and the lack of the variant-transcript in mRNA isolated from patient derived leukocytes (Verselis_2000). The variant was absent in 251342 control chromosomes (gnomAD). c.993+1delG has been reported in the literature in a large family, in multiple family members affected with various tumors belonging to the Li-Fraumeni Syndrome tumor spectrum (Verselis_2000); this family met the classic Li-Fraumeni syndrome criteria, and the variant co-segregated with the disease in multiple family members. These data indicate that the variant is likely to be associated with disease. One submitter (i.e. ClinGen TP53 Variant Curation Expert Panel) has provided clinical-significance assessments for this variant in ClinVar after 2014, and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

​The c.993+1delG intronic pathogenic mutation results from a deletion of the first nucleotide after coding exon 8 of the TP53 gene. This mutation tracked with disease in a large family with multiple members diagnosed with a wide spectrum of Li-Fraumeni related cancers. RT-PCR analyses showed that this alteration, referred to as IVS9+1delG, led to exon 9 skipping (Verselis SJ et al. Oncogene. 2000 Aug 31;19(37):4230-5). In addition to the clinical data presented in the literature, since alterations that disrupt the canonical splice donor site are typically deleterious in nature, this alteration is interpreted as a disease-causing mutation (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294).

This sequence change affects a splice site in intron 9 of the TP53 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TP53 are known to be pathogenic (PMID: 20522432). This variant is not present in population databases (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Studies have shown that disruption of this splice site is associated with altered splicing resulting in unknown protein product impact (PMID: 10980596). ClinVar contains an entry for this variant (Variation ID: 428898). This variant is also known as IVS9+1delG. Disruption of this splice site has been observed in individual(s) with clinical features of Li-Fraumeni syndrome (PMID: 10980596, 31970404). It has also been observed to segregate with disease in related individuals.