ClinVar Miner

Submissions for variant NM_014646.2(LPIN2):c.1510C>T (p.Leu504Phe) (rs104895500)

Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 7
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000221897 SCV000604117 uncertain significance not specified 2016-10-27 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000762223 SCV000892502 uncertain significance not provided 2018-09-30 criteria provided, single submitter clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000084067 SCV000898799 uncertain significance Majeed syndrome 2018-11-30 criteria provided, single submitter clinical testing LPIN2 NM_014646.2 exon 10 p.Leu504Phe (c.1510C>T): This variant has not been reported in the literature but has been reported in 1 individual with psoriasis in the Infevers database (https://infevers.umai-montpellier.fr/web/detail_mutation.php). This variant is present in 0.3% (470/129044) of European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/18-2929103-G-A). This variant is present in ClinVar (Variation ID:97814). Evolutionary conservation suggests that this variant may impact the protein; computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
GeneDx RCV000221897 SCV000279008 uncertain significance not specified 2017-03-27 criteria provided, single submitter clinical testing The L504F variant in the LPIN2 gene has been reported in an individual with psoriasis (personal communication with an external expert, 2008), but, to our knowledge, has not been reported in an individual diagnosed with Majeed syndrome. The L504F variant is observed in 225/66638 (0.34%) alleles from individuals of non-Finnish European background in the ExAC dataset, and no individuals were reported to be homozygous (Lek et al., 2016). However, this variant has been detected in the homozygous state in two presumably healthy individuals tested at GeneDx. The L504F variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Leucine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret L504F as a variant of uncertain significance.
Invitae RCV000084067 SCV000645163 likely benign Majeed syndrome 2018-01-03 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000221897 SCV000539546 uncertain significance not specified 2016-03-29 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: Gene has limited evidence for disease association. Variant is in disease database based on personal communication. Frequency 0.33%
Unité médicale des maladies autoinflammatoires, CHRU Montpellier RCV000084067 SCV000116190 not provided Majeed syndrome no assertion provided not provided

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.