ClinVar Miner

Submissions for variant NM_000302.4(PLOD1):c.1650G>A (p.Thr550=) (rs201999965)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000525113 SCV000631701 uncertain significance Ehlers-Danlos syndrome, hydroxylysine-deficient 2016-10-31 criteria provided, single submitter clinical testing This sequence change affects codon 550 of the PLOD1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the PLOD1 protein. It also falls at the last nucleotide of exon 15 of the PLOD1 coding sequence. This variant is present in population databases (rs201999965, ExAC 0.06%) but has not been reported in the literature in individuals with a PLOD1-related disease. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may alter RNA splicing, but this prediction has not been confirmed by published transcriptional studies. In summary, this is a rare silent change with uncertain impact on splicing. It has been classified as a Variant of Uncertain Significance.
Mendelics RCV000525113 SCV001135174 uncertain significance Ehlers-Danlos syndrome, hydroxylysine-deficient 2019-05-28 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000525113 SCV001255494 uncertain significance Ehlers-Danlos syndrome, hydroxylysine-deficient 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.

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