ClinVar Miner

Submissions for variant NM_001875.5(CPS1):c.1030A>G (p.Thr344Ala) (rs1047883)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000116829 SCV000168021 benign not specified 2013-07-25 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
PreventionGenetics,PreventionGenetics RCV000116829 SCV000308492 benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000116829 SCV000332075 benign not specified 2015-06-10 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000364698 SCV000426823 benign Congenital hyperammonemia, type I 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.
Integrated Genetics/Laboratory Corporation of America RCV000589181 SCV000697872 benign not provided 2017-05-14 criteria provided, single submitter clinical testing Variant summary: The CPS1 c.1030A>G (p.Thr344Ala) variant located in the glutamine amidotransferase domain (via InterPro) involves the alteration of a non-conserved nucleotide and 2/3 in silico tools (MutationTaster not working at time of scoring and SNPsandGo had a low reliability index, therefore, not captured here) predict a benign outcome. However, these for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 68398/120062 control chromosomes (19535 homozygotes) at a frequency of 0.569689, which is approximately 360 times the estimated maximal expected allele frequency of a pathogenic CPS1 variant (0.0015811), suggesting this variant is likely a benign polymorphism. Furthermore, the observed frequency indicates that the varant of interest is the major allele in the general population. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "likely benign/benign." Taken together, this variant is classified as benign.
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000364698 SCV000744162 benign Congenital hyperammonemia, type I 2017-05-31 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000116829 SCV000150903 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000364698 SCV000734167 benign Congenital hyperammonemia, type I no assertion criteria provided clinical testing

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