ClinVar Miner

Submissions for variant NM_014646.2(LPIN2):c.1456+4C>G (rs373685201)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000322162 SCV000408477 uncertain significance 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, 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 RCV000322162 SCV001157858 uncertain significance Majeed syndrome 2018-10-02 criteria provided, single submitter clinical testing The LPIN2 c.1456+4C>G variant (rs373685201), to our knowledge, is not reported in the medical literature or in gene-specific databases. The variant is reported in the ClinVar database (Variation ID: 326638) and in the South Asian population with an overall allele frequency of 0.05% (16/30744 alleles, including 1 homozygotes) in the Genome Aggregation Database. This is an intronic variant, the nucleotide at this position is not conserved, and computational algorithms predict this variant may impact splicing by creating a novel donor splice site (Alamut v.2.11). Considering available information, the clinical significance of this variant is uncertain. Pathogenic LPIN2 variants are causative for autosomal recessive Majeed syndrome (MIM: 609628).

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