Submission Details

The relationship between NDUFAF6 and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of June 20, 2024. NDUFAF6 encodes NADH:ubiquinone oxidoreductase (complex I) assembly factor 6. Defects of this protein lead to a complex I deficiency. This curation was performed in close collaboration with the ClinGen Tubulopathy Gene Curation Expert Panel (GCEP) given that a unique renal phenotype, Acadian variant of Fanconi syndrome, has been reported in association with NDUFAF6 variants in Acadians, a founder population in Nova Scotia, Canada (PMIDs: 17690917, 27466185). Of note, many individuals from this population are now living in Quebec in Canada, and Maine and Louisiana in the United States.

NDUFAF6 was first reported in relation to autosomal recessive primary mitochondrial disease in 2008 (PMID: 18614015). While various names have been given to the constellation of features seen in those with NDUFAF6-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the NDUFAF6 phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework. Of note, NDUFAF6 was first curated by this Expert Panel for its association with Leigh syndrome spectrum (LSS) on April 20, 2020 (SOP V7), with a final classification of Definitive. This current curation for the association with primary mitochondrial disease includes the cases included in the LSS curation.

Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included eight variants (four missense, two nonsense or frameshift variants resulting in premature truncation, two variants impacting splicing) in seven probands from seven publications (PMIDs: 18614015, 27466185, 27623250, 28639102, 29531337, 30642748, 31967322). While the maximum case level score was reached, there have been four additional cases reported in these publications. Therefore, a total of 13 variants have been identified in the 12 cases reported to date (seven missense, three nonsense or frameshift, three variants impacting splicing).

Affected individuals have a spectrum of clinical features including LSS, developmental delay and/or regression, ataxia, exercise intolerance, dystonia, muscle weakness, hypertonia, seizures, and lactic acidosis. Complex I deficiency has been noted in skeletal muscle and fibroblasts.

As noted above, individuals have also been reported with an Acadian variant of Fanconi syndrome, a unique constellation of features that includes infantile onset generalized proximal tubular dysfunction, slowly progressive chronic kidney disease, and pulmonary interstitial fibrosis. Individuals with this phenotype are homozygous for a deep intronic variant shown to result in aberrant splicing (NM_152416.3; c.298-768 T>C). Of note, while not yet reported in the medical literature, members of this Expert Panel knew of additional cases who were compound heterozygous for this variant in addition to a different variant who did not have the Acadian variant of Fanconi syndrome phenotype but rather a multiorgan system disorder.

The mechanism of disease is loss of function. This gene-disease association is also supported by the known biochemical function of NDUFAF6 in complex I assembly, as well as functional alteration in patient and non-patient cells, rescue in patient cells, and a fruit fly model (PMIDs: 38720117, 26741492, 18614015, 23509070, 37364055).

In summary, there is definitive evidence to support the relationship between NDUFAF6 and primary mitochondrial disease. This relationship has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease and Tubulopathy Gene Curation Expert Panels on June 20, 2024 (SOP Version 10).