ClinVar Miner

Submissions for variant NM_001144869.3(LIPT2):c.89T>C (p.Leu30Pro)

gnomAD frequency: 0.00005  dbSNP: rs539962457
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
SIB Swiss Institute of Bioinformatics RCV000505526 SCV000787444 likely pathogenic Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities 2018-04-16 criteria provided, single submitter curation This variant is interpreted as a Likely Pathogenic, for Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities, Autosomal Recessive inheritance. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS3 => Well-established functional studies show a deleterious effect (PMID:28757203). PM3 => For recessive disorders, detected in trans with a pathogenic variant (PMID:28757203).
OMIM RCV000505526 SCV000599792 pathogenic Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities 2017-09-15 no assertion criteria provided literature only
PreventionGenetics, part of Exact Sciences RCV004755942 SCV005346629 uncertain significance LIPT2-related disorder 2024-05-16 no assertion criteria provided clinical testing The LIPT2 c.89T>C variant is predicted to result in the amino acid substitution p.Leu30Pro. This variant was reported together with second variant in an individual with severe neonatal encephalopathy and deleterious effect of this genotype was confirmed in patients fibroblasts (Habarou et al. 2017. PubMed ID: 28757203; Lebigot et al. 2017. PubMed ID: 28803783). This variant is reported in 0.011% of alleles in individuals of African descent in gnomAD. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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