ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3306C>G (p.Tyr1102Ter)

dbSNP: rs879254092
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV003742677 SCV000647440 pathogenic Familial adenomatous polyposis 1 2023-11-08 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr1102*) in the APC gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 1742 amino acid(s) of the APC protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with familial adenomatous polyposis (FAP) (PMID: 1316610, 18224684). ClinVar contains an entry for this variant (Variation ID: 469916). This variant is expected to disrupt the EB1 and HDLG binding sites, which mediate interactions with the cytoskeleton (PMID: 15311282, 17293347). While functional studies have not been performed to directly test the effect on APC protein function, this suggests that disruption of the C-terminal portion of the protein is functionally important. A different truncation (p.Tyr2645Lysfs*14) that lies downstream of this variant has been determined to be pathogenic (PMID: 9824584, 1316610, 27081525, 8381579, 22135120, Invitae). 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.
Ambry Genetics RCV002456175 SCV002612137 pathogenic Hereditary cancer-predisposing syndrome 2022-11-10 criteria provided, single submitter clinical testing The p.Y1102* pathogenic mutation (also known as c.3306C>G), located in coding exon 15 of the APC gene, results from a C to G substitution at nucleotide position 3306. This changes the amino acid from a tyrosine to a stop codon within coding exon 15. This alteration was identified in 1/79 unrelated patients with a clinical diagnosis of familial adenomatous polyposis (FAP) (Miyoshi Y et al. Proc. Natl. Acad. Sci. U.S.A., 1992 May;89:4452-6), as well as 1/108 unrelated Russian FAP patients (Tsukanov AS et al. Russ J Genet. 2017;53(3):356-63). This alteration is expected to result in loss of function by premature protein truncation. As such, this alteration is interpreted as a disease-causing mutation.
Myriad Genetics, Inc. RCV003337309 SCV004044043 pathogenic Familial adenomatous polyposis 1 2023-05-08 criteria provided, single submitter clinical testing This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.

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