Submissions for variant NM_000038.6(APC):c.1958G>A (p.Arg653Lys)

dbSNP: rs1060503318

Total submissions: 4

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000491686	SCV000579851	pathogenic	Hereditary cancer-predisposing syndrome	2022-06-03	criteria provided, single submitter	clinical testing	The c.1958G>A pathogenic variant (also known as p.R653K) is located in coding exon 14 of the APC gene. This variant results from a G to A substitution at nucleotide position 1958. The amino acid change results in arginine to lysine at codon 653, an amino acid with highly similar properties. This change occurs in the last base pair of coding exon 14 which makes it likely to have some effect on normal mRNA splicing. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. This alteration, as well as a close match alteration, c.1958G>T, has been detected in multiple patients with FAP (Azzopardi D et al. Cancer Res. 2008 Jan 15;68(2):358-63; Minde DP et al. Mol Cancer. 2011 Aug 22;10:101; ). RNA studies have demonstrated that this alteration, as well as a close match alteration, c.1958G>T, results in abnormal splicing in the set of samples tested (Ambry internal data; Lagarde A et al. J. Med. Genet., 2010 Oct;47:721-2; Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Invitae	RCV003535776	SCV000768098	pathogenic	Familial adenomatous polyposis 1	2023-12-05	criteria provided, single submitter	clinical testing	This sequence change affects codon 653 of the APC mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the APC protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with familial adenomatous polyposis and colorectal cancer (PMID: 18199528, 20685668, 24599579, 25590978). ClinVar contains an entry for this variant (Variation ID: 428128). 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 15 (also known as exon 14) and introduces a new termination codon (PMID: 20685668, 24599579). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000759416	SCV000888725	pathogenic	not provided	2020-10-08	criteria provided, single submitter	clinical testing	This variant has been reported in in individuals with colorectal adenomas in the published literature (PMIDs: 18199528 (2008) and 20685668 (2010)). This variant also causes exon 15 skipping (PMID: 20685668 (2010)). Additional analysis using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper APC mRNA splicing . Therefore, the variant is classified as pathogenic.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001354779	SCV001549475	pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The APC p.Arg653Lys variant was identified in 7 of 15446 proband chromosomes (frequency: 0.0005) from individuals or families with familial colorectal adenomas and colorectal cancer and was not identified in 1938 control chromosomes from healthy individuals (Azzopardi 2008, Inra 2015, Lagarde 2010). The variant was also identified in ClinVar (classified as pathogenic by Invitae; as likely pathogenic by Ambry Genetics), Cosmic (4x in large intestine), LOVD 3.0 (1x as affects function), and in UMD-LSDB (8x causal) databases. The variant was not identified in dbSNP, COGR, MutDB, or Zhejiang University databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Arg653 residue is conserved across mammals and other organisms, and 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 p.Arg653Lys variant occurs in the last three bases of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In addition, in vitro analysis by RT-PCR and ex vivo analysis by Splicing reporter minigene pCAS, showed major loss of exon 14 during splicing (Grandval 2014). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.