3-Methyl Glutaconic Aciduria and Elevated Plasma Growth Differentiation Factor 15 Level in an Adult with Monoallelic SPG7 Pathogenic Variant

Abstract

Pathogenic variants in SPG7 cause autosomal dominant progressive muscular atrophy. SPG7 encodes an inner mitochondrial membrane protein, paraplegin. Burgeoning lines of evidence have continued to suggest important roles for paraplegin in mitochondria function. Here we report elevated levels of biochemical markers of mitochondria dysfunction [3-methylglutaconic acid and 3-methylglutaric acid (in urine and blood) as well as plasma Growth Differentiation Factor 15 (GDF 15)] in a 65-year-old woman with a heterozygous pathogenic SPG7 variant [c.1529C > T (p.Ala510Val)], and evidence of muscle disease as well as chronic cerebral vasculopathy.

Introduction

Paraplegin is an inner mitochondrial membrane protein that is encoded by SPG7 (MIM 607259), which is located on chromosome 16q24.3. Pathogenic variants in SPG7 have been associated with autosomal recessive spastic paraplegia type 7, autosomal dominant optic atrophy, and autosomal dominant progressive muscular atrophy ^1-5. The biological functions of paraplegin are yet to be fully defined. Preliminary studies have suggested that paraplegin may play important roles in mitochondria function ⁶. Paraplegin complexes with an ATPase, AFG3L2, that plays important roles in mitochondrial quality control ² Inactivation of the paraplegin-AFG3L2 complex has been associated with reduced mitochondria complex I activity ⁷. SPG7 pathogenic variants have also been associated with a reduction in citrate synthase-corrected complex I and complex II/III activities in muscle as well as complex I activity in cultured myoblasts ⁸. Deficiency of respiratory chain complex IV has been observed in yeast cells with impaired AFG3L2 activity ⁹. Two SPG7 variants, c.2102A > C and c.1053dup, have been associated with mitochondrial DNA damage in muscle samples ^10,11. Using histological findings in muscle, a recent study by Jimoh et al. 2025 showed evidence of mitochondrial dysfunction in patients with one of the most common heterozygous pathogenic SPG7 variants [c.1529C > T, p.Ala510Val] ¹². Here we report biochemical markers [blood, urine and muscle tissue] of mitochondria dysfunction in an adult with a heterozygous pathogenic SPG7 variant [p.Ala510Val], and evidence of muscle disease.

Materials and methods

We investigated the pattern of biochemical markers of mitochondria dysfunction in a 65-year-old woman, who was diagnosed in genetics clinic with autosomal dominant SPG7-related progressive muscular atrophy in the setting of an 18-month history of progressive muscle weakness in the lower extremities bilaterally and atrophy of the right calf resulting in wheelchair use. She also reported orthopnea that progressed to persistent dyspnea. Her past medical history included bilateral cataracts, thoracic aortic aneurysm, dilated pulmonary artery, arrhythmia, diabetes type 2, hypertension, hip and knee arthropathies, and osteoma. The patient’s family history appears non-contributory. Physical examination showed atrophy of the right thigh and calf. The optic disc margins appeared sharp with no concerns of optic atrophy. The remainder of her cranial nerve examination was within normal limits. She appeared hypotonic in the upper and lower limb except for the left lower limb that was hypertonic. Her muscle strength was low across myotomes in upper and lower limb. Except for left-sided hyperreflexia in the lower limb, her deep tendon reflexes were hypoactive. There were no fasciculations noted. Proprioception, vibration and temperature sensation was diffusely impaired in the upper and lower limb. She required support to get-up from a seated position. She had an antalgic as well as a moderately wide base gait. She had a negative Romberg test. Babinski sign was positive. Overall, her clinical presentation did not fit into a single neurologic localization (i.e. there were findings of upper and lower motor neuron dysfunction, peripheral neuropathy, and myopathy).

Results and discussion

Creatine kinase levels were within normal limits (Tab. II). Autoimmune and paraneoplastic testing performed at Mayo Clinic Laboratories (MCL) was negative (Tab. III). Pyruvate concentration in the blood was elevated at 1.8 mg/dL [reference range, 0.7-1.4 mg/dL (Tab. II)]. Pulmonary function testing showed a restrictive pattern with a forced vital capacity of 76%. MRI of the brain suggested chronic cerebral vasculopathy (Fig. 1A), consistent with previous observations in patients with SPG7-related disorders ^13,14. MRI of the cervical and thoracic spine demonstrated multilevel degenerative changes that were associated with moderate to severe cervical canal stenosis (at the level of C5-C6) with no intrinsic spinal cord deformity (Fig. 1B). Electrodiagnostic studies [including electromyogram (EMG)] revealed diffuse neurogenic changes and myopathic appearing motor unit potentials (Tab. II).

Table II.

Summary of clinical biochemistry test results.

Analyte	Level or Activity in Blood or Urine	Reference Interval (RI)
Creatine Kinase (Blood)	41 U/L	26 – 192 U/L
Biotinidase Enzyme Activity (Blood)	6.9 U/L	3.5 – 13.8 U/L
Lactate (Blood)	2.1 mmol/L	0.5 to 2.2 mmol/L
Pyruvate (Blood)	1.8 mg/dL (H)	0.7 to 1.4 mg/dL
Growth and Differentiation Factor 15 (Blood)	913 pg/ml (H)	< = 750 pg/mL
3-Methylglutaconic acid (Urine)	44.13 mg/g Cr (H)	2.99 – 3.86 mg/g Cr
n-Tiglylglycine (Urine)	3.93 mg/g Cr (H)	1.06 – 1.67 mg/g Cr
3-Methylcrotonylglycine (Urine)	0.66 mg/g Cr (H)	0.30 – 048 mg/g Cr
n-Hexanoylglycine (Urine)	3.12 mg/g Cr (H)	0.42 – 0.95 mg/g Cr
n-Octanoylglycine (Urine)	1.17 mg/g Cr (H)	0.22 – 0.85 mg/g Cr
Suberylglycine (Urine)	3.39 mg/g Cr (H)	0.43 – 1.57 mg/g Cr
H (high), L (low).

Table III.

Results of autoimmune and paraneoplastic tests.

Analyte	Result
Encephalopathy, Interpretation, S	Negative
AMPA-R Ab CBA, S	Negative
Amphiphysin Ab, S	Negative
Anti-Glial Nuclear Ab, Type 1	Negative
Anti-Neuronal Nuclear Ab, Type 1	Negative
Anti-Neuronal Nuclear Ab, Type 2	Negative
Anti-Neuronal Nuclear Ab, Type 3	Negative
CASPR2-IgG CBA, S	Negative
CRMP-5-IgG, S	Negative
DPPX Ab CBA, S	Negative
GABA-B-R Ab CBA, S	Negative
GAD65 Ab Assay, S	Negative
GFAP IFA, S	Negative
mGluR1 Ab IFA, S	Negative
IgLON5 CBA, S	Negative
LGI1-IgG CBA, S	Negative
Neurochondrin IFA, S	Negative
NIF IFA, S	Negative
NMDA-R Ab CBA, S	Negative
Purkinje Cell Cytoplasmic Ab Type 1	Negative
Purkinje Cell Cytoplasmic Ab Type 2	Negative
Purkinje Cell Cytoplasmic Ab Type Tr	Negative
PDE10A Ab IFA, S	Negative
Septin-7 IFA, S	Negative
TRIM46 Ab IFA, S	Negative

Figure 1.

Axial T2-FLAIR sequence of brain MRI showing hyperintense lesion in the right corona radiata (white arrow) consistent with chronic cerebral vasculopathy (A) as previously described in patients with SPG7-related disorders ^13,14. Axial T2 sequence of cervical spine MRI showing evidence of broad posterior disc osteophyte complex (white arrow) leading to moderate to severe cervical canal stenosis with no intrinsic spinal cord deformity at the level of C5-C6 (B). Abbreviations: FLAIR: fluid attenuated inversion recovery; MRI: magnetic resonance imaging.

A custom gene panel test including genes associated with neuromuscular disorders, neuropathies, amyotrophic lateral sclerosis, neurometabolic disorders, nuclear mitochondrial disorders and others, was performed by Invitae Laboratory (https://www.invitae.com/). The custom gene panel test revealed heterozygous pathogenic variants in SPG7 [NM_003119.4, c.1529C > T (p.Ala510Val)] and BTD [NM_000060.3, c.1330G > C (p.Asp444His)]. The custom gene panel also showed heterozygous variants of uncertain significance in MYH11 [NM_001040113.1, c.36G > T (p.Lys12Asn)], ARCN1 [NM_001655.4, c.614T > C (p.Ile205Thr)], DTNA [NM_001390.4, c.1249C > T (p.Arg417Trp)], KCNA5 [NM_002234.3, c.309C > T (Silent)], PLEC [NM_000445.4; NM_201378.3, c.7823G > A (p.Arg2608Gln)], RYR1 [NM_000540.2, c.4292C > T (p.Thr1431Met)], SQSTM1 [NM_003900.4, c.1277C > T (p.Ala426Val)], TINF2 [NM_001099274.1, c.1307C > T (p.Ala436Val)] and, TOP1MT [NM_052963.2, c.1190G > A (p.Arg397Gln)]. BTD-related disorder is known to be an autosomal recessive disorder ¹⁵. Consistently, her biotinidase enzyme activity was found to be within normal limits (Tab. II). SPG7 c.1529C > T (p.Ala510Val) is a known pathogenic variant ¹⁶. The patient’s parents were deceased and there were no other family members available for genetic testing.

Urine organic acid analysis performed at MCL showed elevations of lactic acid, 3-methyl glutaconic acid and 3-methylglutaric acid. Urine acylcarnitine analysis for 3-hydroxyisovalerylcarnitine/2-methyl 3-hydroxy butyrylcarnitine (C5-OH) was normal. Urine acylglycine analysis confirmed the elevated excretion of 3-methyl glutaconic acid (Tab. II). In keeping with the findings in urine, metabolomic profiling studies in plasma via Global Metabolomic Assisted Pathway Screen test [performed at Baylor Genetics Laboratory (https://www.baylorgenetics.com/global-maps/) via Metabolon, Inc (Durham, NC) as previously described using a reference library that contains entries for around 2,500 unique human metabolites] showed elevated levels of 3-methylglutaconate (Z score = 3.2) and 3-methylglutarylcarnitine (Z score = 3.3) in blood.

Gene panel test for 3-methyl glutaconic aciduria (3MGA) at MCL (https://www.mayocliniclabs.com/test-catalog/overview/608034) did not detect reportable variants in the queried genes suggesting that the elevated levels of 3-methyl glutaconic acid and 3-methylglutaric acid in the patient were less likely to be associated with one of the well-recognized genetic causes of 3MGA. The 3MGA gene panel included: AGK, ATP5F1E, ATPAF2, AUH, CLPB, CPS1, DNAJC19, GFER, HMGCL, HTRA2, OPA3, POLG, SERAC1, SUCLA2, TAZ, TIMM50, and TMEM70. Whole genome sequencing with mitochondrial genome sequencing (performed at Prevention Genetics Laboratory, https://www.preventiongenetics.com/) did not show any additional variants that might potentially explain the patient’s medical history [including the biochemical findings of persistent 3MGA, with levels of 3-methyl glutaconic acid in urine being over 10 times the upper limit (Tab. II)]. Random lactate level in blood was around the upper limit or normal at 2.1 mmol/L (0.5 to 2.2 mmol/L), while pyruvate level in blood was elevated at 1.8 mg/dL (0.7 to 1.4 mg/dL). Given that plasma levels of lactate and pyruvate are not always accurate biomarkers for mitochondria dysfunction ¹⁷, plasma Growth and Differentiation Factor 15 (GDF) 15 was subsequently measured. In parallel with 3MGA, plasma (GDF) 15 was found to be elevated at 913 pg/ml (reference range, < = 750 pg/mL) [Tab. II]. GDF-15 has been shown to be elevated in patients with mitochondria disorders and proposed to be a biomarker for mitochondria disorders ¹⁸. Taken together, these biochemical findings raised concern for mitochondrial dysfunction. Left gluteus maximus biopsy was performed given the EMG and biochemical test results. Histopathology results suggested possibly mixed myopathic and neurogenic processes. Few ragged red fibers and cytochrome c oxidase negative fibers were observed.

Electron transport chain studies demonstrated reduced complex IV (cytochrome c oxidase) activity relative to the control population mean value (Tab. IV), however citrate synthase activity was also very low. Given that paraplegin forms a complex with AFG3L2, the reduced complex IV activity found in our patient may be consistent with previous findings from studies that showed deficiency of respiratory chain complex IV in yeast cells with impaired AFG3L2 activity ⁹. The drastically low levels of citrate synthase relative to control population mean may suggest accelerated age-related decline in skeletal muscle oxidative capacity ^19,20. Sequencing of mitochondrial genome from left gluteus maximus muscle sample at MCL was subsequently performed, which showed no pathogenic or likely pathogenic variants or variants of uncertain significance. Our findings suggest that SPG7-related disorder may manifest with 3MGA and mitochondria dysfunction consistent with previous studies ^6,7,11,21. Our observations and the recent work of Jimoh et al. 2025 ²¹, may also suggest that an improved understanding of paraplegin’s roles may help enhance the current understanding of mitochondria function. The precise cause of 3MGA and mitochondria dysfunction in SPG7-related disorder is currently unclear. Metabolomic profiling showed elevated levels of Tricarboxylic acid (TCA) cycle intermediates and acylcarnitines (Tab. V), which may suggest decreased Krebs cycle flux and intramitochondrial accumulation of acetyl CoA as well reduced fatty acid beta-oxidation ²².

Table IV.

Electron Transport Chain (ECT) Studies in Muscle Specimen. ECT complex activities were normalized against citrate synthase.

Electron Transport Chain (ECT) Activities	ECT Complexes	Patient [% of Mean (nmol/min/mg protein)]	Control ± SD (nmol/min/mg protein)
NADH Ferricyanide Dehydrogenase	1	438 (122, 257)	360.4 ± 96.3
NADH Cytochrome c Reductase	1+11
Total		27.2 (95, 202)	28.4 ± 6.1
Rotenone Sensitive		3.6 (41, 87)	8.7 ± 3.9
Succinate Dehydrogenase	11	35.5 (370, 780)	9.6 +3.0
Succinate-Cytochrome c Reductase	11+111	6.1 (146, 308)	4.2 ±1.2
Cytochrome c Oxidase	1V	28.3 (70, 148)	40.3 ±15.5
*Citrate Synthase		139 (47, 100)	293.1 ±68.0
The ETC enzyme activities are presented in table 1 above with percentage derivatives in parentheses. The first numbers between parentheses in table 1 represent a percentage of mean enzyme activities in the patient relative to control without normalization against citrate synthase, while the second numbers between parentheses represent a percentage of the mean after normalization. Since the activity of all these enzymes are normalized against citrate synthase, which is very low, the percentage enzyme activities generally appear high.

Table V.

Elevated levels of Tricarboxylic acid (TCA) cycle intermediates and acylcarnitines.

Analyte Detected at Increased Level in the Patient’s Blood Sample	Z-score	Human Metabolome Database (HMDB) Code
Alpha-ketoglutarate	2.9	HMDB0000208
Aconitate [cis or trans]	2.2	HMDB0000958
Fumarate	2.1	HMDB0000134
Myristoleoylcarnitine (C14:1)’	2.6	HMDB0240588
Laurylcarnitine (C12)	2.5	HMDB000225
3-hydroxysebacate	2.5	HMDB0000350
Hexanoylcarnitine (C6)	2.4	HMDB0000756
Oleoylcarnitine (C18:1)	2.2	HMDB0005065

Although 3MGA occurs in SERAC1-associated hereditary spastic paraplegia, a disorder arising from mitochondrial membrane protein dysfunction ²³, this is the first report of 3MGA in a patient with SPG7 pathogenic variant. 3MGA is well known to occur in a growing number of monogenic disorders, especially conditions that are associated with generalized mitochondrial dysfunction or mitochondria membrane defects ²⁴. Together with other studies ²¹, our findings provide preliminary, yet translational evidence supporting a crucial role for SPG7 in mitochondria homeostasis.

Funding

The authors have no conflicts of interest to declare.

Conflict of interest statement

The authors declare no conflict of interest.

Authors contributions

Conceptualization- M.A.O.; S.S.; E.Y.H.; B.A.O. Methodology-M.A.O.; K.I.D.; E.Y.H.; S.S.; J.B.T.; S.A.J.;D.K.G. Data Analysis- M.A.O.; K.I.D.; E.Y.H.; S.S.; J.B.T.; S.A.J.;D.K.G. Writing (original draft)-B.A.O.; Writing (reviewing and editing): B.A.O.; M.A.O.; K.I.D.; E.Y.H.; S.S.; JBT.; S.A.J.; D.K.G. Supervision- M.A.O. Guarantor-M.A.O.

Ethical consideration

The study was conducted under an institutional approved protocol.

Consent to participate

Informed consent was obtained from the patient for the study. Informed consent was obtained from the patient for publication.

History

Received: August 11, 2025

Accepted: November 5, 2025

Figures and tables

Table I.

Findings from electrodiagnostic studies, nerve conduction studies and needle-electromyography (EMG).