ClinVar Miner

Submissions for variant NM_014646.2(LPIN2):c.1735T>C (p.Ser579Pro) (rs150022314)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000222234 SCV000279011 likely benign not specified 2017-11-02 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 RCV000271785 SCV000408476 likely benign Majeed syndrome 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000271785 SCV000604116 uncertain significance Majeed syndrome 2018-10-21 criteria provided, single submitter clinical testing The LPIN2 c.1735T>C;p.Ser579Pro variant (rs150022314), to our knowledge, has not been described in the literature or in gene-specific databases. The variant is listed in the ClinVar database (Variation ID: 234339) and in the European (Non-Finnish) population with an allele frequency of 0.4% (548/126436 alleles, including 3 homozygotes) in the Genome Aggregation Database. Additionally, computational programs (PolyPhen-2, SIFT) predict this variant to have no effect on protein function. However, this is not sufficient evidence to assume the variant is benign. Taken together, the clinical significance of this variant is uncertain.
Invitae RCV000271785 SCV000645164 benign Majeed syndrome 2019-12-31 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000271785 SCV000743505 likely benign Majeed syndrome 2014-10-09 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000271785 SCV000744776 likely benign Majeed syndrome 2016-07-25 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000755295 SCV000892501 likely benign not provided 2018-04-01 criteria provided, single submitter clinical testing

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