Mitochondrial DNA depletion syndrome (MDS) includes various disorders characterized by genetic and clinical diversity, marked by a reduction in affected tissues mitochondrial DNA (mtDNA) copies, leading to diminished synthesis of mitochondrial respiratory chain complexes (1). Nuclear genes implicated in MDS include TK2, DGUOK, RRM2B, POLG, MPV17, MGME1, C10orf2, FBXL4, SUCLA2 and SUCLG1 (2, 3).

Pathogenic variants in SUCLA2 have been associated with mitochondrial DNA depletion syndrome, type 5 (MTDPS-5, OMIM ID: 612073) (4). The SUCLA2 gene is approximately 60 kb in length and is responsible for encoding 463 amino acids within the β-subunit of the ADP-forming succinyl-CoA ligase (SUCL-A), a key Krebs cycle enzyme. In the citric acid cycle, this enzyme plays a crucial role in the reversible conversion of succinyl-CoA to succinate. Succinyl-CoA synthase disrupts its tight interaction with mitochondrial nucleoside diphosphate kinase, thereby compromising mitochondrial DNA synthesis and leading to depletion of mitochondrial DNA. It also stabilizes mitochondrial nucleotide diphosphokinase (NDPK), involved in the dNTP salvage pathway in mtDNA replication (5, 6). SUCLA2 protein is primarily expressed in cardiac, skeletal muscle, and cerebral tissues (7, 8). Pathogenic variants in SUCLA2 lead to MTDPS-5 disease characterized by neurosensory deafness, early hypotonia, severe developmental delay, progressive neurological decline, muscle contractures, and dystonia/athetosis. These variants often result in mild increases in plasma lactate, elevations in plasma carnitine esters and methylmalonic acid, and urinary excretion of methylmalonic acid. Cerebral imaging reveals anomalies in the basal ganglia (e.g., caudate and putamen nuclei) and occasional demyelination (4, 9–16). Nowadays, Next-Generation Sequencing (NGS) allows cost-effective and timely assessment of the human genome in small families or individuals, facilitating the study of genotype-phenotype interactions in genetically and clinically diverse diseases such as mitochondrial dysfunction.

In this case, we present a Chinese family exhibiting a rare and severe early progressive encephalomyopathy, diagnosed with mitochondrial DNA depletion syndrome, type 5 (MTDPS-5), and carrying compound heterozygous variants (c.1234C>T; g.48569263–48571020del1758insATGA) in the SUCLA2 gene. The predominant symptoms observed in most patients included hypotonia, severe encephalopathy, generalized dystonia, muscle contractures, feeding difficulties, lack of voluntary movement, deafness as well as elevated levels of lactate and methylmalonic acid in plasma. Our manuscript aligns with the focus of the selected journal and its specific field.

Variants in SUCLA2 are exceptionally rare, with only 56 reported cases documented to date. Upon reviewing previous cases, no instances of mild clinical disease presentation were found (Supplementary Table S1). Typically, symptoms in previous MTDPS-5 patients manifest shortly after birth. This study focuses on two Chinese patients from the familial background who are affected by SUCLA2 (c.1234C>T; g.48569263–48571020del1758insATGA) variants. These patients exhibited symptoms at 4–5 months of age, including hypotonia, severe encephalopathy, generalized dystonia, muscle contractures, feeding difficulties, lack of voluntary movement, and deafness. MRI scans showed hyperintensity within the basal ganglia and bilateral cortical atrophy in these patients. Elevated lactate levels in plasma, along with increased urinary excretion of acetylcarnitine, MMA, and C4DC, were noted in these patients; however, the magnitudes of these metabolic abnormalities was not particularly significant. Furthermore, their symptoms were consistent with those seen in prior patients carrying SUCLA2 variants associated with TCA cycle defects. Neuromuscular symptoms coupled with a mild elevation of MMA and lactate levels in both plasma and urine, are typically seen in MTDPS-5 patients resulting from such variants. Variants in SUCLA2 have been reported in a limited number of individuals, primarily originating from the Faroe Islands, where a frameshift variant (c.534 + 1G>A) within intron 4 is prevalent, leading to exon 4 skipping and premature stop codon formation in most individuals (9, 17). Elpeleg et al. (4) initially reported on two Muslim siblings harboring a homozygous indel variant (c.789_802 + 29delinsATAAA). Carrozzo et al. (10) also documented a case of a Turkish individual carrying a homozygous nonsense variant (c.750C>A) within SUCLA2. These patients presented severe early-onset encephalopathy accompanied by deafness, with alterations observed within basal ganglia structures as well as feeding difficulties, hypotonia, generalized dystonia, muscle contractures, lack of voluntary movement, and mild MMA. The phenotypes observed in our patients resemble those of individuals with loss-of-function variants (deletions, nonsense, and frameshift variants). However, it is worth noting that pathogenic missense variants may retain some residual enzyme activity. As a result, MTDPS-5 patients harboring distinct missense variants of SUCLA2 exhibit a comparatively milder phenotype. Furthermore, the survival rate among affected individuals with missense variants surpasses that of those with loss-of-function variants (median survival age 21 years versus 15 years) (9–11, 15, 18).

Variants in SUCLA2 genes related to mtDNA synthesis may impact the mtDNA content. Although muscle mtDNA content remained consistent, the parents declined invasive diagnostic procedures. Previous studies have utilized blood-extracted DNA to assess mtDNA levels in individuals with SUCLA2 gene variants (19). However, given the age-related decline in blood mtDNA content, we employed blood samples from age-matched healthy children as controls (20). Moreover, our results revealed a notable reduction in mtDNA levels in the affected siblings compared to controls of similar age. Blood samples have specificity but lack sensitivity in detecting mtDNA depletion. Therefore, blood mtDNA content evaluation is only indicative but not diagnostic. Following on the ACMG guidelines, these variants were identified as disease-causing. The indel variant g.48569263–48571020del1758insATGA is located at the exon 2-IVS2 junction of the SUCLA2 gene and may lead to cDNA truncation, resulting in a potential truncation of 77–89 amino acids. Since the ATP-grasp domain is created by amino acids 61–288, with 77–89 amino acids located within the domain, truncation of the peptide chains may lead to changes in protein structure. The c.1234C>T variant may result in the premature stop codon which can be also a consequence of non sense mediated mRNA decay (NMD). However, structural modeling based on a template protein structure suggested also that the lack of this stretch may induce a conformational change (Supplementary Figure S1). A comparison of the wild type of SUCLA2 protein structure (WT), g.48569263–48571020del1758insATGA (MT-1) variant demonstrated a significant transformation from an α-helix and β-fold to an elongated loop (highlighted in red). The c.1234C>T (MT-2) variant exhibited the loss of two α-helices and β-fold at the protein’s C-terminal (highlighted in black), while an additional α-helix appears at amino acid positions 301–307 (highlighted in red).

Based on the clinical presentation, patients with MTDPS-5 exhibit similarities to individuals with methylmalonic aciduria, particularly in terms of elevated metabolites. These “atypical” cases of methylmalonic aciduria are likely associated with SUCLA2 variants. To address this, a more comprehensive genomic testing approach involving single-gene testing, WES, and WGS can be employed. In this study, data on the g.48569263–48571020del1758 variant obtained from WES and WGS were retrospectively compared using IGV visualization software (Supplementary Figure S2). The g.48569263–48571020del1758 variant was not detected by WES due to its location in the 5′ end exon 2, where only a 43 bp region of this variant is present. These findings highlight the potential of WGS in diagnosing diseases that were previously challenging to classify. At present, the MTDPS-5 patient is undergoing symptomatic treatments, including physical therapy to preserve muscle function and prevent joint contractures, antiepileptic drugs, scoliosis and kyphosis bracing, and blepharoplasty. Unfortunately, there are no disease-modifying treatments or established clinical guidelines for managing MTDPS-5. Due to the absence of a definitive diagnosis, the proband has solely undergone physical therapy for muscle function preservation and explored the effectiveness of specific neuro-nutritional medications, which, unfortunately, proved ineffective. For the long-term monitoring of these siblings, coenzyme Q10 supplementation is recommended to improve muscle weakness; however, their parents have declined further specialized care. Subsequently, limited information indicates that PI is currently 9 years old, with no additional details provided. Unfortunately, PII passed away at 1.5 years of age due to respiratory infection.

This clinical case contributes to the understanding of the genotype-phenotype correlation in MTDPS-5 by reporting two novel variants responsible for the condition in Chinese family, thereby raising awareness for this rare disease.

The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.

The studies involving humans were approved by the Ethics Committee of Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital. The studies were conducted in accordance with the local legislation and institutional requirements. Written informed consent for participation in this study was provided by the participants’ legal guardians/next of kin. Written informed consent was obtained from the individual(s), and minor(s)’ legal guardian/next of kin, for the publication of any potentially identifiable images or data included in this article.

XZ: Validation, Methodology, Investigation, Writing – original draft, Conceptualization. GZ: Writing – original draft, Conceptualization. LC: Writing – original draft, Data curation. WZ: Writing – original draft, Validation, Methodology, Investigation. CT: Writing – original draft, Resources. SM: Writing – original draft, Formal analysis. JY: Writing – review & editing, Conceptualization.