ClinVar Miner

Submissions for variant NM_001375808.2(LPIN2):c.698C>T (p.Thr233Ile)

gnomAD frequency: 0.00013  dbSNP: rs139654849
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000687638 SCV000815218 uncertain significance Majeed syndrome 2022-10-25 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 233 of the LPIN2 protein (p.Thr233Ile). This variant is present in population databases (rs139654849, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with LPIN2-related conditions. ClinVar contains an entry for this variant (Variation ID: 567527). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000687638 SCV001160145 uncertain significance Majeed syndrome 2018-12-18 criteria provided, single submitter clinical testing The LPIN2 c.698C>T; p.Thr233Ile variant (rs139654849), 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: 567527) and in the general population with an allele frequency of 0.1% (27/281554 alleles) in the Genome Aggregation Database. The amino acid at this position is weakly conserved and computational algorithms (PolyPhen-2, SIFT) predict this variant is tolerated. Considering available information, the clinical significance of this variant cannot be determined with certainty.
Mayo Clinic Laboratories, Mayo Clinic RCV001507394 SCV001712928 uncertain significance not provided 2020-05-19 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002263931 SCV002543592 uncertain significance Autoinflammatory syndrome 2021-08-11 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000687638 SCV003817032 uncertain significance Majeed syndrome 2023-09-11 criteria provided, single submitter clinical testing

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