Functional Screening of NDUFAF6 Variants in Knockout Cells and Complementary Computational Analysis

NDUFAF6 (NADH:ubiquinone oxidoreductase complex assembly factor 6) is a nuclear-encoded gene essential for the assembly of mitochondrial respiratory chain complex I (NADH:ubiquinone oxidoreductase), the largest and most intricate component of the oxidative phosphorylation system, and its mutations are associated with mitochondrial diseases. However, the functional consequences of many NDUFAF6 variants remain unclear.

We selected 24 NDUFAF6 variants from published studies and our internal sequencing database. Using CRISPR-Cas9, we generated NDUFAF6 knockout HEK293FT cells and transfected them with wild-type or mutant expression vectors. Functional validation was performed using a luminescence-based ATP assay under mitochondrial stress. In silico predictions were conducted using multiple tools, and ColabFold, MitoFates, and ProtScale were used for structural modeling, mitochondrial targeting analysis, and hydrophobicity profiling.

Six variants (p.Pro26fs, p.Asp69Val, p.Arg113Ter, p.Leu193Ter, p.Arg303Ter, and p.Lys331Arg) failed to restore ATP levels in knockout cells, indicating a significant loss of function. Among these, p.Asp69Val and p.Arg113Ter were consistent with ClinVar classifications. However, other variants such as p.Arg303Ter and p.Lys331Arg also showed functional impairment, highlighting discrepancies between database annotations and experimental results. Most variants retained mitochondrial targeting features, though p.Pro26fs exhibited a shifted MPP cleavage site. Hydrophobicity analysis indicated structural instability in several variants.

Our study highlights the importance of experimental validation in improving the classification of NDUFAF6 variants. The ATP-based functional assay provides a useful and quantitative approach for assessing mitochondrial variant effects, which may complement in silico predictions and contribute to future efforts in mitochondrial disease diagnostics.