ClinVar Miner

Submissions for variant NM_000302.4(PLOD1):c.1533C>G (p.Tyr511Ter) (rs121913552)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000621102 SCV000739556 pathogenic Cardiovascular phenotype 2017-07-11 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Alterations resulting in premature truncation (e.g.reading frame shift, nonsense)
Baylor Miraca Genetics Laboratories, RCV000015447 SCV000807212 pathogenic Ehlers-Danlos syndrome, hydroxylysine-deficient 2017-09-01 criteria provided, single submitter clinical testing This variant has been previously reported as disease-causing and was found once in our laboratory in trans with a pathogenic variant in a 4-year-old female with tall habitus, hyperextensibility, hip dysplasia, mild scoliosis, lumbar kyphosis, arachnodactyly, fragile connective tissue, motor delays, hypotonia, dysmorphisms, tethered cord, eye anomalies
GeneDx RCV000255839 SCV000322474 pathogenic not provided 2017-05-04 criteria provided, single submitter clinical testing The Y511X pathogenic variant in the PLOD1 gene has been reported previously in both the compound heterozygous and homozygous state in several individuals with Ehlers-Danlos syndrome type VI (Yeowell et al., 1997; Yeowell et al., 2000; Walker et al., 1999). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The Y511X variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret Y511X as a pathogenic variant.
Invitae RCV000015447 SCV000631697 pathogenic Ehlers-Danlos syndrome, hydroxylysine-deficient 2018-08-08 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr511*) in the PLOD1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs121913552, ExAC 0.01%). This variant has been reported in individuals affected with Ehlers-Danlos syndrome type VI (PMID: 9220536, 10329027). ClinVar contains an entry for this variant (Variation ID: 14370). Loss-of-function variants in PLOD1 are known to be pathogenic (PMID: 21699693, 10874315). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000015447 SCV000035712 pathogenic Ehlers-Danlos syndrome, hydroxylysine-deficient 2000-09-01 no assertion criteria provided literature only

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