ClinVar Miner

Submissions for variant NM_000038.6(APC):c.4876C>T (p.Pro1626Ser)

dbSNP: rs876660610
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000213555 SCV000278178 uncertain significance Hereditary cancer-predisposing syndrome 2015-09-06 criteria provided, single submitter clinical testing The p.P1626S variant (also known as c.4876C>T), located in coding exon 15 of the APC gene, results from a C to T substitution at nucleotide position 4876. The proline at codon 1626 is replaced by serine, an amino acid with similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6502 samples (13004 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.003% (greater than 32000 alleles tested) in our clinical cohort. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of p.P1626S remains unclear.
Invitae RCV003743675 SCV004384544 uncertain significance Familial adenomatous polyposis 1 2023-08-14 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt APC protein function. ClinVar contains an entry for this variant (Variation ID: 233742). This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 1626 of the APC protein (p.Pro1626Ser).

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