ClinVar Miner

Submissions for variant NM_002230.4(JUP):c.777C>T (p.Gly259=) (rs34890640)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000039088 SCV000062766 benign not specified 2012-09-14 criteria provided, single submitter clinical testing Gly259Gly in Exon 05 of JUP: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue, is not located within t he splice consensus sequence and has been identified in 1.7% (63/3738) of Africa n American chromosomes from a broad population by the NHLBI Exome Sequencing Pro ject (http://evs.gs.washington.edu/EVS; dbSNP rs34890640).
GeneDx RCV000039088 SCV000168906 benign not specified 2014-01-27 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.
Invitae RCV001081340 SCV000560957 benign Naxos disease; Arrhythmogenic right ventricular cardiomyopathy, type 12 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589047 SCV000699469 benign not provided 2016-09-05 criteria provided, single submitter clinical testing Variant summary: The JUP c.777C>T (p.Gly259Gly) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 184/121102 control chromosomes (5 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0167598 (174/10382). This frequency is about 1676 times the estimated maximal expected allele frequency of a pathogenic JUP variant (0.00001), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories have classified this variant as benign. The variant of interest has been reported in one sample with carcinoma of large intestine as a somatic occurrence without strong evidence for pathogenicity (COSMIC). Taken together, this variant is classified as Benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000589047 SCV000885626 benign not provided 2018-06-20 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV000769495 SCV000900890 benign Cardiomyopathy 2016-06-17 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001122072 SCV001280752 likely benign Arrhythmogenic right ventricular cardiomyopathy, type 12 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV001122073 SCV001280753 uncertain significance Naxos disease 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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