ClinVar Miner

Submissions for variant NM_000310.4(PPT1):c.363-4G>A (rs117284255)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000118046 SCV000152373 likely benign not specified 2013-08-27 criteria provided, single submitter clinical testing
GeneDx RCV000675772 SCV000171171 benign not provided 2018-11-28 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 21990111, 27535533, 27553520, 30548430)
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000118046 SCV000230065 benign not specified 2014-11-05 criteria provided, single submitter clinical testing
Invitae RCV000225917 SCV000284563 benign Neuronal ceroid lipofuscinosis 1 2020-12-08 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000225917 SCV000357398 benign Neuronal ceroid lipofuscinosis 1 2018-03-06 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.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000118046 SCV000540105 benign not specified 2016-03-28 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency
Broad Institute Rare Disease Group, Broad Institute RCV000118046 SCV000574526 benign not specified 2016-11-20 criteria provided, single submitter reference population ACMG Criteria: BA1.Two heterogous patients with neuronal ceroid lipofuscinosis phenotype were reported (but no second variant identified in these cases) (PMID: 21990111) for this rare, severe, pediatric-onset, autosomal recessive disorder. In ExAC, allele frequency >5% for Latinos, with 27 homozygotes.
Ambry Genetics RCV000716235 SCV000847073 benign History of neurodevelopmental disorder 2016-03-24 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Broad Institute Rare Disease Group, Broad Institute RCV001258248 SCV001435162 benign Central core myopathy criteria provided, single submitter research The heterozygous c.363-4G>A variant in PPT1 has been identified in 2 Turkish individuals with neuronal ceroid lipofuscinosis and no other variants identified in the gene (PMID: 21990111), and has been identified in >5% of Latino chromosomes and 27 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for autosomal recessive infantile neuronal ceroid lipofuscinosis.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000225917 SCV000734027 benign Neuronal ceroid lipofuscinosis 1 no assertion criteria provided clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000675772 SCV000801493 likely benign not provided 2017-10-26 no assertion criteria provided clinical testing
Natera, Inc. RCV000225917 SCV001464022 benign Neuronal ceroid lipofuscinosis 1 2020-09-16 no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000675772 SCV001807315 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000675772 SCV001932147 likely benign not provided no assertion criteria provided clinical testing

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