Submission Details

The TIMM50 gene was first reported in relation to 3-methylglutaconic aciduria in 2017 (Shahrour et al., PMID: 27573165). Several other affected individuals have since been identified, frequently presenting within the first four months of life with infantile spasms, global developmental delay, hypotonia, and failure to thrive. Other phenotypes associated with this syndromic disorder include neurological issues such as hypsarrhythmia, brain atrophy, and optic atrophy, as well as molecular phenotypes characteristic of mitochondrial dysfunction such as 3-methylglutaconic aciduria, serum lactic acidosis, and decreased enzymatic activity of various mitochondrial complexes. Seizures, EEG abnormalities, and psychomotor development appear to be responsive to antiepileptic drugs such as vigabatrin (PMID: 32369862). Patients often exhibit cardiac problems such as left ventricular hypertrophy or dilated cardiomyopathy, and one patient passed away due to cardiorespiratory arrest at age 32 months (PMID: 30190335). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found the molecular mechanism and mode of inheritance (autosomal recessive) to be consistent among unrelated patients, while the phenotypic variability among them appeared to represent a spectrum of disease rather than separate disease entities. Therefore, cases caused by inherited TIMM50 variants have been lumped into a single disease entity, referred to as 3-methylglutaconic aciduria type IX (MONDO:0044724, MIM #617698). Six suspected pathogenic variants were scored as part of this curation (one nonsense and five missense), which have been collectively reported in five probands in four publications (PMID: 27573165, PMID: 30190335, PMID: 32369862, PMID: 31058414). Three probands were homozygous for their respective variants, and were reported to have consanguineous parents (PMID: 27573165, PMID: 32369862). Two other probands were compound heterozygotes within the TIMM50 locus (PMID: 30190335, PMID: 31058414). Minimal segregation evidence was available in these publications, and did not contribute to the scoring of the gene-disease relationship. This gene-disease relationship has not been studied in case-control studies at the single variant level or aggregate variant level. The mechanism of pathogenicity appears to be biallelic loss of function, characterized in some cases by a decrease in the amount of the gene product (PMID: 30190335). All probands found for this curation harbored two variant alleles within the TIMM50 locus. This gene-disease association is also supported by experimental evidence that the TIMM50 protein localizes to the inner mitochondrial membrane and functions as a key component of the TIM23 translocase complex responsible for closing and re-opening the channel to allow selective import of nuclear-encoded proteins into the mitochondria (PMID: 12437925). Yeast models of Tim50 depletion and deletion have identified this yeast ortholog of human TIMM50 as required for nuclear protein import into mitochondria and for yeast cell growth, matching both the decreased activity of mitochondrial complexes and the growth failure shown by the human patients (PMID: 12437925). A mouse model of Tim50 knockout recapitulates key features of the human patients, including exacerbation of surgically-induced cardiomyopathy and enzymatic defects in the mitochondrial respiratory chain (PMID: 28432072). The importance of TIMM50 loss-of-function in the disease mechanism is confirmed by evidence that TIMM50 knockout in a non-patient cell line triggers a defect in cellular respiration (PMID: 31058414). This is consistent with mitochondrial abnormalities observed in immortalized skin fibroblasts derived from patients with 3-methylglutaconic aciduria who harbor TIMM50 variants, who exhibit reductions in respiratory capacity, the number of mitochondrial cristae, and detectable levels of supercomplexes associated with oxidative phosphorylation (PMID: 31058414). Finally, these patient-derived immortalized skin fibroblasts exhibit reduced mitochondrial membrane potential, deficiency in mitochondrial import of proteins such as TFAM, defects in oxygen consumption, reduced cell size, slow growth rate, and high percentage of apoptotic cells (PMID: 30190335). All of these phenotypes can be rescued by lentiviral introduction and expression of wild-type TIMM50 (PMID: 30190335). Many of these experiments have been independently confirmed in the literature, and additional available experimental evidence (PMID: 12574118, PMID: 19144822) was not scored since maximum scoring in this category had already been reached. In summary, the evidence of TIMM50 association with 3-methylglutaconic aciduria type IX has led to a calculated classification of moderate. The body of experimental evidence characterizing the function of TIMM50 in regulating nuclear protein import is particularly strong and well-validated in the literature. While the number of published probands with 3-methylglutaconic aciduria type IX is limited, the use of genome-wide methods to identify their pathogenic TIMM50 variants has successfully excluded other potential genetic causes. These factors have motivated the gene curation expert panel to propose upgrading its association with 3-methylglutaconic aciduria type IX from moderate to strong. This association has been repeatedly demonstrated in both research and diagnostic settings, and has been upheld over time without the emergence of contradictory evidence, leading to a Definitive classification.