ClinVar Miner

Submissions for variant NM_133259.4(LRPPRC):c.58C>T (p.Leu20Phe) (rs184339274)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000126659 SCV000170168 benign not specified 2013-12-26 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.
Illumina Clinical Services Laboratory,Illumina RCV000382726 SCV000430642 uncertain significance Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000757441 SCV000885666 likely benign not provided 2017-09-16 criteria provided, single submitter clinical testing The p.Leu20Phe variant (rs184339274) has not been previously associated with a mitochondrial disorder and is listed in the ClinVar database as benign (Variation ID: 138149). Although this variant is rare in the general population, it is listed in the Genome Aggregation Database (gnomAD) browser with an allele frequency of 2.1% in the African population (identified in 220 out of 10,694 chromosomes with 4 homozygotes). This variant also affects a weakly conserved amino acid (Alamut software v 2.9), and is not predicted to alter LRPPRC structure/function (SIFT: tolerated, PolyPhen2: benign, MutationTaster: polymorphism). Therefore, based on the available evidence, the LRPPRC variant is classified as likely benign.
Invitae RCV000757441 SCV001114150 benign not provided 2020-12-03 criteria provided, single submitter clinical testing
Natera, Inc. RCV000382726 SCV001458058 likely benign Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type 2019-11-11 no assertion criteria provided clinical testing

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