A patient with homozygous nonsense variants in two Leigh syndrome disease genes

Distinguishing a dual diagnosis from a hypomorphic protein-truncating variant

Nicole J. Lake, Luke E. Formosa, David A. Stroud, Michael T. Ryan, Sarah E. Calvo, Vamsi K. Mootha, Bharti Morar, Peter G. Procopis, John Christodoulou, Alison G. Compton, David R. Thorburn

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Leigh syndrome is a mitochondrial disease caused by pathogenic variants in over 85 genes. Whole exome sequencing of a patient with Leigh-like syndrome identified homozygous protein-truncating variants in two genes associated with Leigh syndrome; a reported pathogenic variant in PDHX (NP_003468.2:p.(Arg446*)), and an uncharacterized variant in complex I (CI) assembly factor TIMMDC1 (NP_057673.2:p.(Arg225*)). The TIMMDC1 variant was predicted to truncate 61 amino acids at the C-terminus and functional studies demonstrated a hypomorphic impact of the variant on CI assembly. However, the mutant protein could still rescue CI assembly in TIMMDC1 knockout cells and the patient's clinical phenotype was not clearly distinct from that of other patients with the same PDHX defect. Our data suggest that the hypomorphic effect of the TIMMDC1 protein-truncating variant does not constitute a dual diagnosis in this individual. We recommend cautious assessment of variants in the C-terminus of TIMMDC1 and emphasize the need to consider the caveats detailed within the American College of Medical Genetics and Genomics (ACMG) criteria when assessing variants.

Original languageEnglish
Pages (from-to)893-898
Number of pages6
JournalHuman Mutation
Volume40
Issue number7
DOIs
Publication statusPublished - 1 Jul 2019

Keywords

  • ACMG guidelines
  • complex I
  • Leigh syndrome
  • protein truncation
  • TIMMDC1

Cite this

Lake, Nicole J. ; Formosa, Luke E. ; Stroud, David A. ; Ryan, Michael T. ; Calvo, Sarah E. ; Mootha, Vamsi K. ; Morar, Bharti ; Procopis, Peter G. ; Christodoulou, John ; Compton, Alison G. ; Thorburn, David R. / A patient with homozygous nonsense variants in two Leigh syndrome disease genes : Distinguishing a dual diagnosis from a hypomorphic protein-truncating variant. In: Human Mutation. 2019 ; Vol. 40, No. 7. pp. 893-898.
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abstract = "Leigh syndrome is a mitochondrial disease caused by pathogenic variants in over 85 genes. Whole exome sequencing of a patient with Leigh-like syndrome identified homozygous protein-truncating variants in two genes associated with Leigh syndrome; a reported pathogenic variant in PDHX (NP_003468.2:p.(Arg446*)), and an uncharacterized variant in complex I (CI) assembly factor TIMMDC1 (NP_057673.2:p.(Arg225*)). The TIMMDC1 variant was predicted to truncate 61 amino acids at the C-terminus and functional studies demonstrated a hypomorphic impact of the variant on CI assembly. However, the mutant protein could still rescue CI assembly in TIMMDC1 knockout cells and the patient's clinical phenotype was not clearly distinct from that of other patients with the same PDHX defect. Our data suggest that the hypomorphic effect of the TIMMDC1 protein-truncating variant does not constitute a dual diagnosis in this individual. We recommend cautious assessment of variants in the C-terminus of TIMMDC1 and emphasize the need to consider the caveats detailed within the American College of Medical Genetics and Genomics (ACMG) criteria when assessing variants.",
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Lake, NJ, Formosa, LE, Stroud, DA, Ryan, MT, Calvo, SE, Mootha, VK, Morar, B, Procopis, PG, Christodoulou, J, Compton, AG & Thorburn, DR 2019, 'A patient with homozygous nonsense variants in two Leigh syndrome disease genes: Distinguishing a dual diagnosis from a hypomorphic protein-truncating variant', Human Mutation, vol. 40, no. 7, pp. 893-898. https://doi.org/10.1002/humu.23753

A patient with homozygous nonsense variants in two Leigh syndrome disease genes : Distinguishing a dual diagnosis from a hypomorphic protein-truncating variant. / Lake, Nicole J.; Formosa, Luke E.; Stroud, David A.; Ryan, Michael T.; Calvo, Sarah E.; Mootha, Vamsi K.; Morar, Bharti; Procopis, Peter G.; Christodoulou, John; Compton, Alison G.; Thorburn, David R.

In: Human Mutation, Vol. 40, No. 7, 01.07.2019, p. 893-898.

Research output: Contribution to journalArticleResearchpeer-review

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AB - Leigh syndrome is a mitochondrial disease caused by pathogenic variants in over 85 genes. Whole exome sequencing of a patient with Leigh-like syndrome identified homozygous protein-truncating variants in two genes associated with Leigh syndrome; a reported pathogenic variant in PDHX (NP_003468.2:p.(Arg446*)), and an uncharacterized variant in complex I (CI) assembly factor TIMMDC1 (NP_057673.2:p.(Arg225*)). The TIMMDC1 variant was predicted to truncate 61 amino acids at the C-terminus and functional studies demonstrated a hypomorphic impact of the variant on CI assembly. However, the mutant protein could still rescue CI assembly in TIMMDC1 knockout cells and the patient's clinical phenotype was not clearly distinct from that of other patients with the same PDHX defect. Our data suggest that the hypomorphic effect of the TIMMDC1 protein-truncating variant does not constitute a dual diagnosis in this individual. We recommend cautious assessment of variants in the C-terminus of TIMMDC1 and emphasize the need to consider the caveats detailed within the American College of Medical Genetics and Genomics (ACMG) criteria when assessing variants.

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