ClinVar Miner

Submissions for variant NM_000310.3(PPT1):c.904A>G (p.Ile302Val) (rs146902902)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000435004 SCV000232942 uncertain significance not provided 2015-03-10 criteria provided, single submitter clinical testing
GeneDx RCV000435004 SCV000242330 uncertain significance not provided 2018-03-08 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the PPT1 gene. The I302V variant has been reported previously as a heterozygous variant in a male individual with hypsarrhythmia, infantile spasms, and developmental delay who also harbored a de novo pathogenic variant in KCNQ2 and a variant in PCDH19 (Millichap et al., 2016). The I302V variant is observed in 218/126,644 (0.17%) alleles from individuals of European background in large population cohorts (Lek et al., 2016). The I302V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Illumina Clinical Services Laboratory,Illumina RCV000515384 SCV000357389 uncertain significance Neuronal ceroid lipofuscinosis 1 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.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000435004 SCV000510906 uncertain significance not provided 2016-07-13 criteria provided, single submitter clinical testing Converted during submission to Uncertain significance.
Fulgent Genetics,Fulgent Genetics RCV000515384 SCV000611426 uncertain significance Neuronal ceroid lipofuscinosis 1 2017-05-23 criteria provided, single submitter clinical testing
Invitae RCV000515384 SCV000640464 likely benign Neuronal ceroid lipofuscinosis 1 2020-01-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV000720864 SCV000851748 likely benign History of neurodevelopmental disorder 2018-08-31 criteria provided, single submitter clinical testing In silico models in agreement (benign) ;Sub-population frequency in support of benign classification (not ava blue, manual h-w)
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000515384 SCV000734025 likely benign Neuronal ceroid lipofuscinosis 1 no assertion criteria provided clinical testing
GenomeConnect, ClinGen RCV000515384 SCV000986819 not provided Neuronal ceroid lipofuscinosis 1 no assertion provided phenotyping only Variant interpretted as Uncertain significance and reported on 05/31/2018 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille RCV001252358 SCV001428112 uncertain significance Intellectual disability 2019-01-01 no assertion criteria provided clinical testing

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