Intellectual disability - microarray and sequencing
Gene: TIMM50Comment on list classification: TIMM50 was added to the ID panel and rated Green by Konstantinos Varvagiannis. Not yet associated with a disorder in Gene2Phenotype but upgraded rating from Grey to Green following review of literature evidence. PMID:27573165 and PMID:31058414 report 5 patients from 3 families with a consistent ID and epilepsy phenotype accompanied by 3-methylglutaconic aciduria. In addition, PMID:30190335 report pyschomotor regression in their patient, and a conference abstract (Serajee et al. 2015) adds an additional case of developmental delay. Therefore ID appears a consistent phenotype of 3-methylglutaconic aciduria and with sufficient reported cases, a Green rating is appropriate.Created: 30 Sep 2019, 2:21 p.m. | Last Modified: 30 Sep 2019, 2:21 p.m.
Panel Version: 2.1054
Summary of evidence (see Konstantinos Varvagiannis' review for details):
Serajee et al. 2015 ASHG conference abstract: A homozygous mutation, Gly372Ser in TIMM50 was reported in three sibs who suffered from intractable epilepsy and developmental delay accompanied by 3-methylglutaconic aciduria.
PMID:27573165 (Shahrour et al., 2017) report 4 patients from 2 unrelated families with severe ID and seizures, and compound het missense variants Arg217Trp and Thr252Met in the TIMM50 gene. Functional assays in yeast could not demonstrate variant pathogenicity.
PMID:30190335 (Reyes et al., 2018) used WES to identify compound het pathogenic variants in TIMM50 (nonsense p.S112* and missense p.G190A) in an infant Italian girl with infantile spasms, early-onset hypotonia, psychomotor regression/stagnation, and severe epilepsy (Supplementary file). Each parent was heterozygous for one variant. The G190A variant occurs in a conserved residue of the protein at the C-terminus and is predicted as damaging by different bioinformatics tools.
PMID:31058414 (Tort et al., 2019) report a 17 year old Spanish boy with 3-MGA-uria. At 3.5 months, West Syndrome was diagnosed (which is characterised by epileptic/infantile spasms, abnormal brain waves and ID). Compound het variants in TIMM50 were identified: p.Arg114Gln and p.Gly269Ser. The mother and father were both carriers.Created: 30 Sep 2019, 2:18 p.m. | Last Modified: 30 Sep 2019, 2:18 p.m.
Panel Version: 2.1053
Biallelic pathogenic TIMM50 variants cause 3-methylglutaconic aciduria, type IX (MIM 617698).
At least 9 affected individuals from 5 unrelated (but often consanguineous) families of variable origin have been reported (based on a conference abstract and PMIDs : 27573165, 30190335, 31058414).
TIMM50 encodes encodes a subunit of the mitochondrial presequence import machinery called the TIM23 complex. TIMM50 serves as a major receptor in the intermembrane space that binds to proteins on their way to cross the mitochondrial inner membrane (summary by Shahrour et al., 2017 and OMIM).
The highly overlapping patient clinical features [seizures, DD and ID - the latter in all age-appropriate individuals (5 from 3 families - refs 2,4)], metabolic investigations (lactate elevations in many, elevated urinary 3MGA in almost all, variable mitochondrial complex deficiencies in some), additional extensive functional evidence of mitochondrial dysfunction or the similar phenotypes in other types of 3-methylglutaconic aciduria all support a role for the gene.
[AUH- / CLPB- / DNAJC19- / HTRA2- / OPA3- / SERAC1-related methylglutaconic acidurias are all included as relevant disorders in the ID panel, with the respective genes rated green.]
TIMM50 is included in gene panels for ID offered by some diagnostic laboratories (incl. Radboudumc and GeneDx).
The gene is not associated with any phenotype in G2P
As a result this gene could be considered for inclusion/upgrade as green in both ID and epilepsy panels respectively.
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[1] - Serajee et al. (ASHG conference 2015 - abstract Nr. 2299T) reported on a patient born to consanguineous parents of South Asian ancestry with intractable epilepsy, microcephaly, DD and spastic quadriplegia. Metabolic investigations revealed increased urinary 3MGA. Two similarly affected sisters with demonstrated increase of 3MGA, were deceased following an infection. WES in the affected child, 2 unaffected sibs and the parents suggested a homozygous missense variant as the likely cause of the disorder in the proband (c.1114G>A / p.G372S - Reference not specified though the variant probably corresponds to ENST00000314349.4 and ClinVar's entry VCV000208697.1 - www.ncbi.nlm.nih.gov/clinvar/variation/208697/).
[2] - Shahroor et al. (2017, PMID: 27573165) reported on 2 consanguineous families, each with 2 affected individuals. Two sibs from the 1st family (of Bedouin origin) presented with seizures (onset at 3m and 4m respectively), DD and ID with slightly elevated plasma lactate and increased urinary 3MGA upon metabolic investigations. Enzymatic activities of mitochondrial complex I-V were carried out for 1 sib and were normal also after normalization for citrate synthase. Following a SNP array, WES was carried out in affected children and their parents. Both sibs were homozygous for a missense SNV [NM_001001563.1:c.755C>T / p.Thr252Met]. Segregation studies - also in 3 unaffected sibs - supported a role for the variant.
Two sibs from the 2nd family (of Muslim origin) presented with seizures (myoclonic jerks at 3m, generalized tonic movements at 2m - respectively) with DD and ID. Urinary 3MGA was elevated for both, with CSF lactate also elevated in one. WES revealed homozygosity for p.Arg217Trp (NM_001001563.1:c.649C>T) and segregation studies in parents and an unaffected sib were again compatible.
The authors could not demonstrate pathogenicity of the variants in a yeast based system although - as also commented on in Ref 4 - the human TIMM50 could not rescue the yeast ΔΤim50 growth defect and global conservation between the two proteins is poor.
[3] - Reyes et al. (2018, PMID: 30190335) reported on one individual with onset of infantile spasms at the age of 2m with hypsarrythmia upon EEG and psychomotor regression. Leigh-like features were noted upon brain MRI. Lactate was elevated in both plasma and CSF. Urinary 3MGA was normal. WES, Sanger confirmation and segregation studies demonstrated compound htz for 2 variants (NM_001001563:c.335C>A or p.S112* and c.569G>C or p.G190A). Functional studies demonstrated among others decrease in all components of the TIM23 complex and decreased mitochondrial membrane potential. Patient fibroblasts grown in glucose had lower levels of all complex II and IV subunits and one complex I subunit (due to the impairment in import system) with decreased mitochondrial respiration and increase in ROS production. Growth in galactose - shifting energy production toward OxPhos - caused massive cell death. The phenotype was rescued/substantially improved following complementation of patient fibroblasts with wt TIMM50.
[4] - Tort et al. (2019, PMID: 31058414) reported on a boy with seizures and ID (diagnosis of West syndrome), Leigh-like MRI anomalies, cardiomyopathy with elevated plasma and CSF lactate and persistent urinary elevation of 3MGA. The proband was found to be compound heterozygous for 2 TIMM50 variants [NM_001001563.5:c.341 G>A (p.Arg114Gln) in trans with c.805 G>A (p.Gly269Ser)] following WES and Sanger confirmation/segregation studies. In patient fibroblasts TIMM50 protein levels were severely reduced upon WB although mRNA levels were similar to control. Muscle biopsy revealed decreased activity of the complexes I-IV, when normalized to the citrate synthase activity. Accumulation of lipidic material in muscle fibers was shown to be associated with mitochondria upon EM. Expression and sublocalization of mitochondria-targeted proteins were not found to be affected in patient fibroblasts. In extracts from muscle biopsy reduced protein levels of SDHA, COX4L and MTCO1 were demonstrated, in line with the disruptions in the activities of the MRC. Mitochondrial morphology and network were shown to be altered in patient fibroblasts. Patient fibroblasts showed marked reduction of max respiratory capacity. Similar reduction was noted in CRISPR/Cas9 generated TIMM50-ko HEK293T cells, but rescued upon transient transfection with a plasmid encoding for wt TIMM50.
(Functional studies better summarized in the respective articles).
Sources: Literature, Radboud University Medical Center, NijmegenCreated: 22 Sep 2019, 12:33 p.m.
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
3-methylglutaconic aciduria, type IX (MIM 617698)
Publications
Variants in this GENE are reported as part of current diagnostic practice
Gene: timm50 has been classified as Green List (High Evidence).
Phenotypes for gene: TIMM50 were changed from 3-methylglutaconic aciduria, type IX (MIM 617698) to 3-methylglutaconic aciduria, type IX, 617698
gene: TIMM50 was added gene: TIMM50 was added to Intellectual disability. Sources: Literature,Radboud University Medical Center, Nijmegen Mode of inheritance for gene: TIMM50 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TIMM50 were set to 27573165; 30190335; 31058414; Serajee et al. (ASHG conference 2015 - abstract Nr. 2299T) Phenotypes for gene: TIMM50 were set to 3-methylglutaconic aciduria, type IX (MIM 617698) Penetrance for gene: TIMM50 were set to Complete Review for gene: TIMM50 was set to GREEN gene: TIMM50 was marked as current diagnostic