ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.4237G>C (p.Asp1413His) (rs183655276)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082249 SCV000114198 likely benign not specified 2015-03-06 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000082249 SCV000246994 uncertain significance not specified 2014-05-01 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000082249 SCV000314551 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000351974 SCV000381452 likely benign Joubert 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 RCV000402012 SCV000381453 uncertain significance Meckel syndrome, type 4 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.
Illumina Clinical Services Laboratory,Illumina RCV000307654 SCV000381454 uncertain significance Leber congenital amaurosis 10 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.
Illumina Clinical Services Laboratory,Illumina RCV000366483 SCV000381455 likely benign Senior-Loken syndrome 6 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 RCV000408211 SCV000381456 likely benign Bardet-Biedl syndrome 14 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.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000442189 SCV000511628 likely benign not provided 2016-09-15 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Invitae RCV001082252 SCV000554515 benign Joubert syndrome; Meckel-Gruber syndrome; Nephronophthisis 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000082249 SCV000566049 uncertain significance not specified 2017-06-14 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the CEP290 gene. The D1413H substitution has been reported previously, as a paternally inherited variant in a patient with autism spectrum disorder who did not have any reported history of brain malformations (Mercati et al., 2016). The NHLBI Exome Sequencing Project reports D1413H was observed in 24/8204 (0.3%) alleles from individuals of European American ancestry and the 1000 Genomes Project reports D1413H was observed in 4/214 (1.9%) alleles from individuals of Iberian background. This substitution occurs at a position where amino acids with similar properties to Aspartic acid are tolerated across species. However, the D1413H 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. In silico analysis is inconsistent in its predictions as to whether or not the variant is 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.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000442189 SCV000780444 uncertain significance not provided 2018-04-01 criteria provided, single submitter clinical testing

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