ClinVar Miner

Submissions for variant NM_004655.4(AXIN2):c.629T>C (p.Met210Thr) (rs529954883)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000355775 SCV000405747 benign Oligodontia-colorectal cancer syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV000355775 SCV000559545 likely benign Oligodontia-colorectal cancer syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000483836 SCV000567091 uncertain significance not specified 2016-12-12 criteria provided, single submitter clinical testing This variant is denoted AXIN2 c.629T>C at the cDNA level, p.Met210Thr (M210T) at the protein level, and results in the change of a Methionine to a Threonine (ATG>ACG). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. AXIN2 Met210Thr was observed with an allele frequency of 0.30% (49/16512) in individuals of South Asian ancestry in the Exome Aggregation Consortium (ExAC) data set. Since Methionine and Threonine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. AXIN2 Met210Thr occurs at a position where amino acids with properties similar to Methionine are tolerated across species and is not located in a known functional domain (Salahshor 2005). In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available evidence, it is unclear whether AXIN2 Met210Thr is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.
Ambry Genetics RCV001025101 SCV001187227 uncertain significance Hereditary cancer-predisposing syndrome 2019-12-23 criteria provided, single submitter clinical testing Insufficient evidence

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