ClinVar Miner

Submissions for variant NM_001194998.2(CEP152):c.2878T>C (p.Trp960Arg) (rs201342438)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000723661 SCV000113615 uncertain significance not provided 2015-03-13 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000145619 SCV000192716 uncertain significance Primary autosomal recessive microcephaly 9 2013-02-15 criteria provided, single submitter clinical testing
GeneDx RCV000723661 SCV000567318 uncertain significance not provided 2016-09-15 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the CEP152 gene. The W960R variant has been reported previously in the heterozygous state in three unrelated individuals with atrioventricular septal defects; however, these individuals did not have features of CEP125-related disorders and did not have a second variant identified in CEP152 (D'Alessandro et al., 2015). The NHLBI Exome Sequencing Project reports W960R was observed in 35/8188 (0.4%) alleles from individuals of European background, and the 1000 Genomes Project reports it was observed in 2/1006 (0.2%) alleles from individuals of European background. The W960R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Fulgent Genetics,Fulgent Genetics RCV000515271 SCV000611448 uncertain significance Seckel syndrome 5; Primary autosomal recessive microcephaly 9 2017-05-23 criteria provided, single submitter clinical testing
Invitae RCV000723661 SCV001117463 likely benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001116508 SCV001274600 likely benign Seckel syndrome 5 2018-01-12 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 RCV000145619 SCV001274601 uncertain significance Primary autosomal recessive microcephaly 9 2018-01-12 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.
Institut de Recherche Interdisciplinaire en Biologie Humaine et Moleculaire,Universite Libre de Bruxelles RCV000145619 SCV000998513 likely pathogenic Primary autosomal recessive microcephaly 9 no assertion criteria provided clinical testing

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