ClinVar Miner

Submissions for variant NM_000038.6(APC):c.385G>C (p.Glu129Gln) (rs376628500)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000196705 SCV000254011 benign Familial adenomatous polyposis 1 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000216893 SCV000273092 uncertain significance Hereditary cancer-predisposing syndrome 2018-11-12 criteria provided, single submitter clinical testing Insufficient or conflicting evidence
Counsyl RCV000196705 SCV000489348 uncertain significance Familial adenomatous polyposis 1 2016-09-26 criteria provided, single submitter clinical testing
GeneDx RCV000120050 SCV000490404 uncertain significance not specified 2016-08-03 criteria provided, single submitter clinical testing This variant is denoted APC c.385G>C at the cDNA level, p.Glu129Gln (E129Q) at the protein level,and results in the change of a Glutamic Acid to a Glutamine (GAA>CAA). This variant has not, to our knowledge, beenpublished in the literature as pathogenic or benign. APC Glu129Gln was not observed at a significant allele frequencyin 1000 Genomes. Since Glutamic Acid and Glutamine differ in some properties, this is considered a semi-conservativeamino acid substitution. APC Glu129Gln occurs at a position that is conserved across species and is not located in aknown functional domain (Azzopardi 2008). In silico analyses are inconsistent regarding the effect this variant mayhave on protein structure and function. Based on currently available information, it is unclear whether APC Glu129Glnis pathogenic or benign. We consider it to be a variant of uncertain significance.
Color RCV000216893 SCV000681635 likely benign Hereditary cancer-predisposing syndrome 2020-04-07 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589545 SCV000694039 likely benign not provided 2016-05-09 criteria provided, single submitter clinical testing Variant summary: The APC c.385G>C (p.Glu129Gln) variant involves the alteration of a conserved nucleotide. 2/4 in silico tools predict a benign outcome (SNPs&GO not captured due to low reliability index). This variant was found in 8/122738 control chromosomes, predominantly observed in the East Asian subpopulation at a frequency of 0.000911 (8/8772). This frequency is about 15 times the estimated maximal expected allele frequency of a pathogenic APC variant (0.0000602), suggesting this is likely a benign polymorphism found primarily in populations of East Asian origin. A clinical diagnostic laboratory classified this variant as Uncertain. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Considering the high prevalence of the variant in the East ASian population, it was classified as Likely Benign.
ITMI RCV000120050 SCV000084186 not provided not specified 2013-09-19 no assertion provided reference population

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