ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1495C>T (p.Arg499Ter) (rs137854580)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000204796 SCV000261001 pathogenic Familial adenomatous polyposis 1 2018-04-09 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg499*) in the APC gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported in patients with familial adenomatous polyposis (PMID: 8381580, 9487968, 20685668, 20223039, 21779980). ClinVar contains an entry for this variant (Variation ID: 824). Loss-of-function variants in APC are known to be pathogenic (PMID: 17963004, 20685668). For these reasons, this variant has been classified as Pathogenic.
Counsyl RCV000204796 SCV000487892 pathogenic Familial adenomatous polyposis 1 2015-11-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV000491830 SCV000579777 pathogenic Hereditary cancer-predisposing syndrome 2017-10-02 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Alterations resulting in premature truncation (e.g.reading frame shift, nonsense)
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000499412 SCV000591076 pathogenic Familial adenomatous polyposis 2016-10-13 criteria provided, single submitter clinical testing
GeneDx RCV000521676 SCV000617335 pathogenic not provided 2017-08-29 criteria provided, single submitter clinical testing This pathogenic variant is denoted APC c.1495C>T at the cDNA level and p.Arg499Ter (R499X) at the protein level. The substitution creates a nonsense variant, which changes an Arginine to a premature stop codon (CGA>TGA), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been reported in patients and families with classical Familial Adenomatous Polyposis (Eccles 1997, Kanter-Smoler 2008, Fostira 2010, Marabelli 2016, Yurgelun 2017) and is considered pathogenic.
Center for Human Genetics, Inc RCV000499412 SCV000781071 pathogenic Familial adenomatous polyposis 2016-11-01 criteria provided, single submitter clinical testing
Color RCV000491830 SCV000905882 pathogenic Hereditary cancer-predisposing syndrome 2017-11-30 criteria provided, single submitter clinical testing
OMIM RCV000000867 SCV000021017 pathogenic Gardner syndrome 1997-11-01 no assertion criteria provided literature only
Yale Center for Mendelian Genomics,Yale University RCV000204796 SCV000784635 pathogenic Familial adenomatous polyposis 1 2015-11-27 no assertion criteria provided literature only

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