Submissions for variant NM_000038.6(APC):c.1548G>C (p.Lys516Asn)

dbSNP: rs879254090

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000236999	SCV000293418	pathogenic	not provided	2022-02-18	criteria provided, single submitter	clinical testing	Variant at the last nucleotide of the exon demonstrated to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease (Lagarde 2010, Grandval 2014); Not observed at significant frequency in large population cohorts (gnomAD); Identified in patients with a personal and/or family history consistent with pathogenic variants in this gene referred for genetic testing at GeneDx and in published literature (van der Luijt 1997, Aretz 2004, Nielsen 2007, Crobach 2012, Liu 2016); This variant is associated with the following publications: (PMID: 15459959, 15300853, 21859464, 20564245, 20223039, 8990002, 27000756, 22000517, 20685668, 17489848, 20513532, 29901124, 22941256, 30414835, 18199528, 24599579)
Ambry Genetics	RCV000491475	SCV000579802	pathogenic	Hereditary cancer-predisposing syndrome	2023-05-24	criteria provided, single submitter	clinical testing	The c.1548G>C pathogenic mutation (also known as p.K516N), located in coding exon 11 of the APC gene, results from a G to C substitution at nucleotide position 1548. The amino acid change results in lysine to asparagine at codon 516, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 11, which makes it likely to have some effect on normal mRNA splicing. This mutation was originally reported in 2 unrelated Dutch FAP families (van der Luijt et al. Hum Mutat. 1997;9(1):7-16), and has since been reported in multiple FAP kindreds to date (Aretz S et al. Hum Mutat. 2004 Nov;24(5):370-80; Nielsen M et al. Clin Genet. 2007 May;71(5):427-33; Crobach S et al. Fam. Cancer 2012 Dec;11(4):671-3; Liu Q et al. Tumour Biol. 2016 Mar). In silico splice site analysis predicts that this alteration will result in the creation or strengthening of a novel splice donor site. However, one study found that a different alteration at the same location, c.1548G>A, caused complete skipping of exon 11 at the mRNA level (Kaufmann A et al. J Mol Diagn. 2009 Mar;11(2):131-9). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Invitae	RCV003535657	SCV000816663	pathogenic	Familial adenomatous polyposis 1	2023-08-17	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 12 (also known as exon 11) and introduces a premature termination codon (PMID: 20685668, 24599579; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 246087). This missense change has been observed in individuals with familial adenomatous polyposis (PMID: 8990002, 15300853, 15459959, 17489848, 20685668, 27000756). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 516 of the APC protein (p.Lys516Asn). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product.
Clinical Genetics and Genomics, Karolinska University Hospital	RCV000236999	SCV001450172	pathogenic	not provided	2016-01-14	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV002519828	SCV004044021	pathogenic	Familial adenomatous polyposis 1	2023-06-15	criteria provided, single submitter	clinical testing	This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 17726045, Myriad internal data]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [19196998, 20685668].
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000501897	SCV000591077	pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The p.Lys516Asn variant was identified in 7 of 3860 proband chromosomes (frequency: 0.002) from individuals or families with FAP or Attenuated-FAP, and was not identified in control chromosomes from healthy individuals (Nielsen 2007, Cowie 2004, Miclea 2010, Aretz 2004 15, van der Luijt 1997). The variant was also identified by our laboratory in 3 individuals with disease status not confirmed. The p.Lys516Asn variant was identified in the UMD Colon Genes database 11x and classified as causal and in the InSIGHT Colon cancer database, the variant was identified 6x and was classified 4x as pathogenic and 2x as unknown. The variant was not identified in the dbSNP nor in NHLBI Exome Sequencing Project (Exome Variant Server), Exome Aggregation Consortium (ExAC) database, COSMIC, MutDB, “Zhejiang Colon Cancer Database”, the ClinVar database, Clinvitae and GeneInsight COGR databases. The p.Lys516 residue is conserved across mammals and lower organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the Asparagine (Asn) variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. The c.1548G>C variant occurs in the last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position can affect splicing. In addition, 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer and HumanSpliceFinder) predict a greater than 10% difference in splicing. In one family, 17 patients were reported, there were more than 2 affected generations and 9 individuals had confirmed colon cancer, 2 had greater than 100 polyps and 10 had 10-100 polyps (Nielsen 2007). In addition, another variant at the same position c.1548G>A, was reported in one individual with FAP and transcript analysis demonstrated that the variant leads to complete skipping of exon 11 of the APC gene (c.1548G>A; r.1409_1548del; p.Gly471Tyrfs*19), increasing the likelihood that the c.1548G>C variant may result in aberrant splicing (Kaufmann 2009). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic.