ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1192_1193del (p.Lys398fs) (rs387906238)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000159588 SCV000209568 pathogenic not provided 2018-09-25 criteria provided, single submitter clinical testing This deletion of 2 nucleotides is denoted APC c.1192_1193delAA at the cDNA level and p.Lys398GlufsX5 (K398EfsX5) at the protein level. The normal sequence, with the bases that are deleted in braces, is TGAC[AA]GAGA. The deletion causes a frameshift, which changes a Lysine to a Glutamic Acid at codon 398, and creates a premature stop codon at position 5 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. APC 1192_1193delAA has been observed in several individuals with a phenotype consistent with Familial Adenomatous Polyposis (Young 1998, Friedl 2005, Crobach 2012). We consider this variant to be pathogenic.
Invitae RCV000000871 SCV000827100 pathogenic Familial adenomatous polyposis 1 2018-05-29 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Lys398Glufs*5) 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 observed to segregate with familial adenomatous polyposis in a family (PMID: 9603437). ClinVar contains an entry for this variant (Variation ID: 828). Loss-of-function variants in APC are known to be pathogenic (PMID: 17963004, 20685668). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000000871 SCV000021021 pathogenic Familial adenomatous polyposis 1 1998-01-01 no assertion criteria provided literature only

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