ClinVar Miner

Submissions for variant NM_001375808.2(LPIN2):c.1154C>T (p.Pro385Leu)

gnomAD frequency: 0.00002  dbSNP: rs754221410
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000521005 SCV000618112 uncertain significance not provided 2017-08-28 criteria provided, single submitter clinical testing The P385L variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is observed in 10/16506 (0.06%) alleles from individuals of South Asian background in the ExAC dataset (Lek et al., 2016). P385L is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV000792434 SCV000931732 uncertain significance Majeed syndrome 2022-09-01 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 385 of the LPIN2 protein (p.Pro385Leu). This variant is present in population databases (rs754221410, gnomAD 0.05%). 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: 449743). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.

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