ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3088A>T (p.Lys1030Ter) (rs587779786)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000115077 SCV000148986 pathogenic not provided 2013-12-30 criteria provided, single submitter clinical testing This is a nonsense variant, denoted APC c.3088A>T at the cDNA level and p.Lys1030Ter (K1030X) at the protein level. The substitution creates a nonsense variant, changing a Lysine to a premature stop codon (AAA>TAA). This variant is predicted to cause loss of normal protein function through protein truncation. Although, this variant has not, to our knowledge, been published in the literature, there are multiple other reports of pathogenic nonsense variants upstream and downstream of this mutation per HGMD.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000115077 SCV000226388 pathogenic not provided 2014-07-17 criteria provided, single submitter clinical testing
Invitae RCV000174976 SCV000552500 pathogenic Familial adenomatous polyposis 1 2016-10-14 criteria provided, single submitter clinical testing This sequence change results in a premature translational stop signal in the last exon of the APC mRNA at codon 1030 (p.Lys1030*). While this is not anticipated to result in nonsense mediated decay, it is expected to delete the last 1814 amino acids (~64%) of the APC protein. While this variant has not been reported in the literature, a different truncation downstream of this variant (p.Arg1114*) has been determined to be pathogenic (PMID: 1338764, 20685668, 20223039, 16134147). This suggests that deletion of this region of the APC protein is causative of disease. For these reasons, this variant has been classified as Pathogenic.

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