Combined homozygous HACE1 and TBCD variants in two siblings with severe early-onset neurodevelopmental disorder: Two case reports

Abstract

BACKGROUND

Spastic paraplegia and psychomotor retardation with or without seizures (spastic paraplegia and psychomotor retardation with or without seizures; MIM #616756) is a rare autosomal recessive neurodevelopmental disorder caused by biallelic pathogenic variants in HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 (HACE1) gene. Mutations in the tubulin-specific chaperone D (TBCD) gene cause progressive early-onset encephalopathy with brain atrophy and a thin corpus callosum (PEBAT; MIM #617193). Approximately 40 cases are documented for each disorder. Despite different mechanisms, HACE1- and TBCD-associated disorders share overlapping features, complicating early differential diagnosis. We report co-occurrence of homozygous variants in HACE1 and TBCD in two brothers with global developmental delay.

CASE SUMMARY

We describe two Chechen brothers born to healthy unrelated parents. The older brother (3 years 10 months) presented with profound global developmental delay, mixed tetraparesis, early-onset epileptic encephalopathy, generalized epilepsy, dysphagia, and protein-energy malnutrition. Brain magnetic resonance imaging revealed marked cerebral/cerebellar atrophy, corpus callosum hypoplasia, gliosis and cystic frontoparietal changes. The younger brother (2 years 2 months) exhibited ataxic cerebral palsy, severe developmental delay, and recurrent febrile episodes. Neuroimaging demonstrated corpus callosum hypoplasia, mild periventricular white matter T2-fluid-attenuated inversion recovery (T2-FLAIR) signal hyperintensities, and compensatory (ex vacuo) enlargement of both ventricles and subarachnoid spaces. Whole-exome sequencing performed in the younger brother identified homozygous truncating HACE1 c.625C>T (p.Gln209*) and a novel homozygous missense TBCD c.2139T>A (p.His713Gln) variants. The older brother shared both homozygous variants; parents were asymptomatic carriers. Although the TBCD variant initially appeared likely pathogenic, in silico predictions and its frequency in the Chechen population led to a likely benign classification, though a potential modifying effect on the disease course cannot be excluded.

CONCLUSION

This family represents combined homozygous HACE1 and TBCD variants in two siblings with severe neurodevelopmental impairment. HACE1 causes the phenotype, while TBCD is likely a neutral ethnicity-specific allele.

Key Words: HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1; Tubulin-specific chaperone D; Spastic paraplegia; Psychomotor retardation; Epileptic encephalopathy; Brain atrophy; Corpus callosum hypoplasia; Neurodevelopmental disorder; Pediatrics; Case report

Core Tip: This report describes two brothers sharing homozygous variants in HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 (HACE1) and tubulin-specific chaperone D (TBCD) genes. Both siblings have severe developmental delay, spastic tetraparesis, early-onset epileptic encephalopathy, and marked cerebral and cerebellar atrophy with corpus callosum hypoplasia, highlighting the challenges of diagnosing overlapping neurogenetic syndromes. Exome testing revealed that they both share the truncating HACE1 c.625C>T variant that explains their clinical symptoms. Conversely, a novel TBCD c.2139T>A allele is likely benign, illustrating the importance of population-specific genetic datasets.

INTRODUCTION

Spastic paraplegia and psychomotor retardation with or without seizures (spastic paraplegia and psychomotor retardation with or without seizures [SPPRS]; MIM: #616756) is a rare autosomal recessive neurodevelopmental disorder caused by biallelic pathogenic variants in the HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 (HACE1) gene. The disorder is characterized by early-onset global developmental delay, hypotonia evolving into spasticity, intellectual disability, epilepsy, and variable structural brain abnormalities, including cerebral atrophy and corpus callosum hypoplasia[1-3]. Since the initial description of HACE1-related disease, only a limited number of affected individuals have been reported worldwide, highlighting the extreme rarity of this condition[1]. A recent comprehensive review further defined the clinical landscape of the disorder by adding 8 new cases from 5 unrelated families, bringing the global total to 40 documented cases across 22 families[4].

Most reports suggest biallelic loss of function as the primary disease mechanism[1-3]. Despite increasing recognition, the clinical spectrum of SPPRS remains poorly defined, and genotype-phenotype correlations are still poorly understood due to the small number of described cases.

Pathogenic variants in the tubulin-specific chaperone D (TBCD) gene cause another rare autosomal recessive neurodevelopmental disorder known as progressive early-onset encephalopathy with brain atrophy and a thin corpus callosum (PEBAT; MIM: #617193)[5]. This condition is characterized by severe developmental delay, early-onset seizures, progressive cerebral atrophy, and abnormalities of the corpus callosum. To date, 41 molecularly confirmed cases of TBCD-related encephalopathy have been reported in the literature, with an estimated prevalence of less than 1 per 1000000[6]. Although the molecular mechanisms differ, HACE1- and TBCD-associated disorders share overlapping clinical and neuroimaging features, which may complicate differential diagnosis in early childhood.

With the increasing use of whole-exome sequencing, the co-occurrence of pathogenic variations affecting multiple loci is being recognized more frequently, particularly in patients with severe early-onset encephalopathy and complex phenotypes[7]. Here, we describe two affected brothers carrying rare homozygous variants in both HACE1 and TBCD.

CASE PRESENTATION

Chief complaints

Case 1: A 3-year-10-month-old Chechen boy was admitted to the psychoneurology department of the St. Petersburg State Pediatric Medical University (Saint Petersburg, Russia) because of severe global developmental delay and recurrent seizures, accompanied by a history of feeding difficulties and episodic unexplained fever.

Case 2: The 3-year-10-month-old Chechen boy’s younger brother.

History of present illness

Case 1: According to parental reports, the proband was born at 39 weeks of gestation by emergency cesarean section due to placental abruption. The pregnancy was complicated by maternal anemia, hyperemesis during the first trimester, herpes labialis in early pregnancy, and oligohydramnios diagnosed at 20 weeks of gestation. Birth weight was 3100 g and length was 49 cm.

Developmental delay became evident within the first months of life, with failure to achieve age-appropriate motor milestones. The child could not sit with support or stand. He had severe language delay and was unable to speak. From approximately 5 months of age, epileptic seizures were noted. Seizure episode frequency and severity progressively increased despite initiation and subsequent escalation of anticonvulsive therapy. Based on the clinical course and electroencephalographic findings, epileptic encephalopathy was suggested. Other possible diagnoses included conditions such as hereditary spastic paraplegias, pontocerebellar hypoplasia, infantile neuronal ceroid lipofuscinosis, organic acidurias, congenital disorders of glycosylation, and mitochondrial disorders.

The clinical course was further complicated by feeding difficulties and severe dysphagia, recurrent respiratory infections, and episodic unexplained febrile episodes not consistently associated with identifiable infectious triggers. Progressive neurological impairment prompted repeated hospitalizations.

Case 2: The younger brother demonstrated a similar neurodevelopmental trajectory, with early-onset global developmental delay and motor impairment. Recurrent febrile episodes of unclear origin were also reported. He received treatment at the E.P. Glinka Republican Children’s Clinical Hospital (Grozny, Russian Federation); medical records from that hospitalization were subsequently reviewed and included in the present analysis.

History of past illness

Case 1: The proband had a history of congenital cytomegalovirus infection documented in early childhood, without evidence of active infection at the time of neurological evaluation. He experienced multiple severe respiratory infections, including pneumonia requiring intensive care treatment and subsequent tracheostomy placement. No history of traumatic brain injury or acute metabolic crises was reported.

Case 2: The younger sibling had no documented congenital infections. His medical history was notable for recurrent respiratory infections and feeding difficulties.

Personal and family history

The parents are of Chechen ethnicity and denied consanguinity. The paternal lineage is reported to belong to both the Sandukhoy and Nashkhoy teips (clans), while the maternal ancestors belong to the Sandukhoy teip. Both parents were clinically unaffected and had no history of epilepsy, intellectual disability, or other hereditary neurological disorders. The mother had two pregnancies, both resulting in live births. The family pedigree is shown in Figure 1.

Figure 1 Pedigree of the family with HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 and tubulin-specific chaperone D variants. Filled symbols indicate affected individuals homozygous for both variants. Symbols with a central dot denote clinically unaffected heterozygous carriers.

A maternal cousin reportedly experienced febrile seizures in early childhood, without subsequent neurodevelopmental impairment. No other family members were known to have neurodevelopmental disorders or epilepsy.

Extended family history revealed no additional neurological disorders; isolated findings included a stillbirth at term on the maternal side (II-4), an early spontaneous miscarriage on the paternal side (III-12), and cerebrovascular death in the paternal grandfather (I-5).

Physical examination

Case 1: On physical examination, the general condition of the proband was moderately severe. Body weight was 14 kg, and height was 102 cm. Vital signs were stable.

The skin and visible mucous membranes were clean. The patient was a tracheostomy carrier. Respiratory examination revealed harsh breath sounds with transmitted upper airway sounds.

Neurological examination revealed profound global developmental delay. The child was conscious but showed minimal responsiveness to external stimuli and did not react to auditory cues. Expressive speech was absent, and no age-appropriate self-care skills were present.

Cranial nerve examination demonstrated symmetrical pupils and preserved light reflexes. Visual tracking was absent. Facial movements were symmetrical, and the tongue was midline. Pseudobulbar signs were present.

Muscle tone was variable, with a predominance of generalized hypotonia and intermittent dystonic posturing. Deep tendon reflexes were symmetrical, with bilateral pathological plantar responses, including a positive Babinski sign and ankle clonus, more pronounced on the left. Assessment of coordination, sensation, and gait was not feasible due to severe motor impairment. Meningeal signs were absent. According to caregivers, epileptic seizures occurred frequently, most often after sleep.

Case 2: The younger brother exhibited severe psychomotor delay and motor impairment consistent with an ataxic cerebral palsy phenotype. Independent sitting and standing were not achieved.

Laboratory examinations

Routine laboratory investigations, including complete blood count, biochemical profile, liver and renal function tests, and inflammatory markers, were largely unremarkable outside episodes of intercurrent infection. Recurrent elevations of C-reactive protein were observed during febrile episodes without a clear infectious source. Immunological screening did not reveal evidence of primary immunodeficiency.

Electroencephalography examinations

During the first hospitalization, the electroencephalography (EEG) recording showed a disorganized background pattern dominated by delta-theta activity with a mean amplitude of 60-80 μV. Moderate interhemispheric amplitude asymmetry (approximately 30%) was observed. No epileptiform discharges or focal abnormalities were detected at that time. Photic stimulation did not induce epileptiform activity.

Upon the second hospitalization, EEG demonstrated marked deterioration of electrophysiological findings. The background activity was severely deformed and disrupted by frequent generalized epileptiform discharges, including diffuse bursts of spike-wave complexes and bilaterally lateralized epileptiform activity occurring asynchronously. The epileptiform activity index exceeded 50%, consistent with epileptic encephalopathy and correlating with the clinically refractory seizure course.

Genetic testing

Whole-exome sequencing with mean coverage of 120 × was performed in the younger sibling by Genomed Laboratory (Moscow, Russia) using the Genoscan4000 device (Sesana LLC, Moscow, Russia). Sanger sequencing was subsequently used for verification of next-generation sequencing findings and familial segregation analysis (Figure 2).

Figure 2 Sanger sequencing. A-D: HACE1 c.625C>T (p.Gln209*) variant: Homozygous in both affected siblings (A and D) and heterozygous in both parents (B and C); E-H: TBCD c.2139T>A (p.His713Gln) variant: Homozygous in both affected siblings (E and H) and heterozygous in both parents (F and G).

A homozygous nonsense variant in HACE1 NM_020771.4: C.625C>T (p.Gln209*) was identified in both affected siblings, while parents were heterozygous carriers free from any symptoms. This variant introduces a premature termination codon, resulting in predicted loss of function of the encoded protein. According to the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology guidelines, the variant fulfills PVS1 (null variant in a gene where loss of function is a known disease mechanism) and PM2 criteria (absence in population databases) and was therefore classified as likely pathogenic. Importantly, while being absent in the publicly available databases including gnomAD v4.1.1, The 1000 Genomes Project, TOPMed, RUSeq, the variant was previously described in homozygous state in a single patient from Saudi Arabia. The girl had severe intellectual disability, developmental delay, microcephaly, hypoplastic corpus callosum and likely brainstem abnormality, small sella with ectopic neurohypophysis, and mild ventriculomegaly. She also had a mildly dysmorphic face, bilateral hip dyslocation, kyphoscoliosis, and ulnar deviation of the wrists and small feet[8]. A detailed comparison of the clinical and neuroimaging features observed in our patients and the previously reported individual carrying the same homozygous HACE1c.625C>T variant is provided in Table 1.

Table 1 Comparison of clinical features in patients homozygous for the HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 c.625C>T (p.Gln209*) variant.

	Clinical features of SPPRS (OMIM #616756)	Patient from Nagy et al[8], 2019	Proband (III-5)	Proband’s younger brother (III-6)
Ethnicity/origin	Pan-ethnic	Saudi Arabia	Chechen	Chechen
Sex	Males and females	Female	Male	Male
Age at presentation	Infancy/early months	5 years 4 months	3 years 10 months	2 years 2 months
Neurology
Sitting and walking	Unsteady waddling gait; inability to walk	Not achieved at 5 years	Not achieved at 3 years	Not achieved at 2 years
Expressive speech	Poor or severely delayed	Absent at 5 years	Absent at 3 years	Absent at 2 years
Developmental delay	Present (severe)	Present	Present	Present
Epilepsy	Seizures (in some patients)	Absent	Present (early-onset epileptic encephalopathy)	Absent
Mobility	Hypotonia; spasticity; ataxia	Hypotonia	Hypotonia evolving into spasticity	Hypotonia
Ophthalmic findings	Strabismus; myopia; retinal dystrophy	Retinal dystrophy	Partial bilateral optic nerve atrophy	Not reported
Hearing	Sensorineural hearing loss (in some patients)	Bilateral sensorineural loss noted at 4 years	Normal	Not reported
Intellectual disability	Present	Present	Present	Present
Brain MRI	Hypoplastic corpus callosum; cerebral atrophy; delayed myelination; decreased white matter volume	Microcephaly and brachycephaly; hypoplastic corpus callosum and likely brainstem abnormality; small sella with ectopic neurohypophysis; mild ventriculomegaly	Progressive cerebral and cerebellar atrophy; thinning of the corpus callosum; cystic changes and gliosis in the left frontoparietal region; ventriculomegaly	Hypoplastic corpus callosum; mild periventricular white matter changes; mixed hydrocephalus
Gastrointestinal	Not reported	Intestinal pseudo-obstruction; neurogenic bladder and bladder stoma	Severe dysphagia; feeding difficulties; protein-energy malnutrition	Feeding difficulties
Skeletal	Kyphosis; scoliosis; hip dislocation; foot deformities	Bilateral hip dislocation; thoracolumbar kyphoscoliosis; ulnar deviation of the wrists, small feet	Normal	Normal
Endocrine	Not reported	Hypothyroidism; adrenal insufficiency	Not reported	Not reported
Facial features	No consistent dysmorphism	Downturned mouth	Normal	Normal

MRI: Magnetic resonance imaging; SPPRS: Spastic paraplegia and psychomotor retardation with or without seizures.

Both affected siblings were also found to carry a homozygous missense variant in TBCD NM_005993.5: C.2139T>A (p.His713Gln), whereas both parents were heterozygous carriers showing no symptoms. This previously unreported variant was classified as a variant of uncertain significance according to ACMG criteria (PM2). Computational and structural analysis supported the non-pathogenic nature of this substitution. Specifically, multiple pathogenicity predictors (including SIFT, PolyPhen-1/2, and PANTHER) uniformly classified the p.His713Gln variant as neutral (Table 2)[9-11]. Comparative structural modeling revealed no significant differences in protein stability or local packing between the wild-type and mutant TBCD proteins (global root mean square deviation = 0.000 Å), suggesting a lack of significant structural or functional impairment. TBCD alterations are associated with progressive early-onset encephalopathy with brain atrophy and a thin corpus callosum, a condition partially overlapping with the neuroimaging features observed in the present cases.

Table 2 Computational pathogenicity scores and calibrated thresholds for the tubulin-specific chaperone D c.2139T>A (p.His713Gln) variant.

Tool	Score	Prediction	Threshold
AlphaMissense	0.1353	Benign	0-0.33[9]
REVEL	0.162	Benign moderate	0.016-0.183[10]
CADD (v1.7)	0.395 (PHRED)	Benign moderate	0.15-17.3[10]
PolyPhen	0.007	Benign moderate	≤ 0.009[10]
SIFT1	0.01	Indeterminate	0.080-0.327 (benign supporting); 0-0.001 (pathogenic supporting)[10]
PANTHER	30 my (0.13 Pdel)	Probably benign	Time < 200 my[11]

¹SIFT result was flagged as “low confidence” due to limited sequence alignment depth.

PHRED: PHRED-scaled score; Pdel: Probability of deleterious effect; my: Million years.

To date this variant was not reported in the gnomAD database thus allowing apply the PM2 argument for pathogenicity. Yet, we detected this variant in heterozygous state in 2 of 58 (3.4%) unrelated healthy donors of Chechen ethnicity; this fact adds the BS1 criterion (allele frequency is greater than expected for the disorder). Thus, we classify the TBCD c.2139T>A allele as “likely benign” (BS1, BP4).

Imaging examinations

Case 1: Brain magnetic resonance imaging: During the first hospitalization, neuroimaging assessment included neurosonography, which demonstrated symmetrical cerebral structures without evidence of mass effect or biventricular dilatation. The lateral ventricles measured up to 22 mm on the right and 18 mm on the left anterior frontal horn width measurements, with Evans index being 0.51. The third ventricle measured 2 mm, and the temporal horns were not dilated. The parenchymal echogenicity of the cerebral cortex and white matter was within normal limits for the child's age, with the thalami and choroid plexuses appearing homogeneous and no additional pathological echo signals detected in the scanning area.

Brain magnetic resonance imaging (MRI) performed during the second hospitalization, more than two years after the initial imaging, revealed progressive brain parenchymal atrophy and ex-vacuo enlargement of ventricles (Figure 3). There was a progression of diffuse cerebral and cerebellar atrophy due to a decrease in the volume of white matter involving both hemispheres and the cerebellar vermis, accompanied by worsening ex-vacuo enlargement of the ventricular system. The corpus callosum was formed in all segments but was significantly thinned.

Figure 3 Brain magnetic resonance imaging of the older brother. A: Axial T1-weighted image showing prominent cortical atrophy and compensatory enlargement of the lateral ventricles; B: Axial T2-weighted image demonstrating global volume loss and widened subarachnoid spaces; C: Axial apparent diffusion coefficient (ADC) map showing no evidence of low ADC value; D: Sagittal T1-weighted image revealing marked thinning (hypoplasia) of the corpus callosum and atrophy of the cerebellum; E: Coronal T1-weighted image highlighting the symmetrical widening of the Sylvian fissures and frontotemporal atrophy; F: Axial diffusion weighted sequence demonstrates absence of acute ischemic lesions. The findings collectively represent progressive cerebral and cerebellar atrophy in this child with spastic paraplegia and psychomotor retardation with or without seizures (SPPRS) phenotype.

Newly developed cystic and gliotic changes were identified in the posterior regions of the left frontal lobe and the anterior regions of the left parietal lobe, measuring approximately 24 mm × 41 mm × 28 mm. The lateral ventricles were moderately enlarged without significant asymmetry, and the third ventricle measured up to 7 mm. No diffusion restriction, focal signal abnormalities, or space-occupying lesions were detected. Midline structures were not displaced; the optochiasmatic region and pituitary gland (including lobular differentiation) appeared unremarkable. Regarding the posterior fossa, the fourth ventricle and basal cisterns were of normal shape and size, the cerebral aqueduct was patent, and the cerebellar tonsils were positioned above the level of the foramen magnum. These findings were consistent with a progressive neurodegenerative process rather than a static encephalopathy.

Case 2: Brain MRI of the younger brother demonstrated milder but concordant abnormalities, including hypoplasia of the corpus callosum, minimal periventricular white matter changes of dystrophic character, ex vacuo enlargement of ventricular system and subarachnoid spaces due to brain atrophy, and enlargement of the basal cisterns.

FINAL DIAGNOSIS

Spastic paraplegia and psychomotor retardation with or without seizures due to biallelic loss-of-function variants in HACE1.

TREATMENT

Case 1

The proband received long-term combined antiseizure therapy, including levetiracetam, valproic acid, vigabatrin, and phenobarbital, with limited seizure control. Supportive management included nutritional support, respiratory care, and rehabilitation therapy. No disease-modifying treatment is currently available.

Case 2

The younger sibling received symptomatic and supportive therapy.

OUTCOME AND FOLLOW-UP

Case 1

Despite intensive supportive and antiseizure therapy, the proband demonstrated progressive neurological deterioration, refractory epilepsy, and worsening structural brain abnormalities on serial MRIs.

Case 2

The younger sibling remains under neurological follow-up with severe developmental delay but less advanced neurodegeneration.

The parents provided informed consent for case report publication.

DISCUSSION

We describe two brothers of Chechen origin with a severe early-onset neurodevelopmental disorder and co-existent homozygous variants in HACE1 and TBCD. The main interpretive challenge in this family is to determine whether the phenotype is fully explained by biallelic loss of HACE1 (SPPRS) or the concomitant TBCD variant may contribute to the severity and progression of neuroimaging and epilepsy.

The first molecular delineation of HACE1 deficiency reported individuals with profound developmental delay and progressive spasticity due to biallelic truncating variants with absence of detectable HACE1 protein, supporting loss of function as the key disease mechanism[1].

In the present family, both affected children were homozygous for HACE1 NM_020771.4: C.625C>T (p.Gln209*), a truncating variant predicted to introduce premature termination and thereby result in loss of function. Importantly, this exact variant has been described in the literature, including a comprehensive genotype-phenotype and mechanistic study using a Hace1 knockout mouse model that recapitulated core clinical and neuroimaging features of SPPRS and linked disease biology to altered Ras-related C3 botulinum toxin substrate 1 signaling and synaptic deficits[8]. There is neither indication that presence of additional TBCD variants segregate with a more severe phenotype nor any evidence of digenic inheritance. This provides strong external support that the HACE1 finding alone offers a robust genetic explanation for the core phenotype in both siblings.

To the best of our knowledge, only one SPPRS case involving a patient from Russia has been described to date; genetic analysis revealed a novel gross deletion of the HACE1[12]. Thus, we report the second and third affected individuals documented within the Russian Federation. Notably, the presence of large deletions in this gene highlights a diagnostic challenge as gross deletions can lead to “pseudo-homozygosity”, a phenomenon where a single-nucleotide variant appears homozygous because the corresponding region on the other allele is entirely deleted[12]. Although the detection of the heterozygous HACE1 c.625C>T variants in both parents in this family confirms true homozygosity, this pitfall remains a critical consideration in situations when parental DNA is unavailable, or results do not align with clinical expectations.

In our proband, a follow-up MRI more than 2 years after the initial study documented progressive cerebral and cerebellar atrophy with secondary enlargement of the brain's ventricles due to the loss of brain tissue and further thinning of the corpus callosum, alongside newly apparent cystic changes and foci of gliosis. In parallel, EEG evolved from nonspecific background disorganization without epileptiform discharges to a markedly abnormal tracing dominated by generalized epileptiform activity with a high epileptiform index, aligning with a clinically refractory epileptic encephalopathy. Together, these longitudinal findings expand the clinical spectrum of SPPRS by emphasizing that, at least in some patients, the disorder may show clear negative dynamics over time, reinforcing the value of repeated neuroimaging and EEG assessment.

In addition to the pathogenic HACE1 variant, both siblings were homozygous for a missense variant in TBCD, classified as a variant of uncertain significance. The TBCD gene encodes tubulin folding cofactor D, which plays a critical role in microtubule assembly and neuronal integrity. Biallelic mutations in TBCD are known to cause PEBAT, a severe neurodegenerative disorder characterized by profound developmental delay, seizures, and progressive diffuse cerebral atrophy[5,6].

Since the original description of TBCD-associated disease, multiple reports have highlighted substantial phenotypic heterogeneity, ranging from rapidly progressive fatal encephalopathy to more variable courses with partial overlap with other neurodevelopmental syndromes[5,6,13-15]. Neuroimaging findings in TBCD-related encephalopathy, particularly progressive cerebral atrophy and marked callosal involvement, overlap with the structural abnormalities observed in the present family. However, in the absence of functional evidence or independent reports implicating the TBCD c.2139T>A (p.His713Gln) variant as pathogenic, a primary causal role for this TBCD variant cannot be established. Despite the homozygous state of the variant, in silico predictions testify against pathogenicity. Moreover, we have found this allele in 2 of 58 unrelated healthy donors of Chechen ethnicity. One may suggest that Chechens may have an unusually high prevalence of PEBAT due to in question founder TBCD variant, but we do not have epidemiological evidence proving this hypothesis.

Given the well-supported pathogenicity of the HACE1 truncating variant, we interpret HACE1 deficiency as the main driver of the clinical phenotype.

With the widespread implementation of whole-exome sequencing, patients with multiple molecular diagnoses are increasingly recognized[7]. Sometimes the researchers may face difficulties with interpretation if rare variants affect genes associated with overlapping phenotypes. Here we provide an example: If the HACE1 variant had not been previously reported as pathogenic we would also suggest a causal role for the TBCD variant.

While medical genetics of the Chechen population remains understudied, there is strong evidence for the existence of founder effect and consanguinity. For example, the prevalence of an autosomal recessive hereditary tyrosinemia type 1 is one of the highest in the world with all the patients being homozygous for the FAH c.1025C>T (p.Pro342 Leu) mutation[16]. Chechens also demonstrated accumulation of specific alleles associated with other recessive conditions like cystic fibrosis[17] and nephropathic cystinosis[18]. Our observation may also indicate persistence of particular HACE1 and/or TBCD variants in this ethnic group.

Clinically, this report emphasizes several key points. First, truncating HACE1 variants should be considered a cause of severe, potentially progressive epileptic encephalopathy. Second, longitudinal MRI and EEG studies are valuable for assessing disease evolution and prognosis. Finally, the report suggests underrepresentation of some ethnicities (like Chechens) in gnomAD database which may lead to possible variant misinterpretation.

CONCLUSION

We report two brothers with a severe early-onset neurodevelopmental disorder caused by a homozygous truncating variant in HACE1, consistent with spastic paraplegia and psychomotor retardation with or without seizures. The disease course was marked by profound developmental impairment, refractory epilepsy, and progressive brain atrophy documented on serial neuroimaging and EEG, extending the clinical spectrum of HACE1-related disease. The additional homozygous TBCD variant may be reclassified as “likely benign” while its role as a disease modifier cannot be completely excluded.