Novel TMEM63A mutation associated with transient hypomyelination of infancy - lessons from a previously negative whole-exome sequencing case: Three case reports

Abstract

BACKGROUND

Hypomyelinating leukodystrophies are rare neurodevelopmental disorders characterized by impaired myelin development and early motor delay. Hypomyelinating leukodystrophy type 19 (HLD-19), also termed transient hypomyelination of infancy, is caused by TMEM63A variants. It can clinically resemble other hypomyelinating leukodystrophies but is distinguished by developmental improvement. However, its phenotypic spectrum remains incompletely defined.

CASE SUMMARY

We describe 3 related individuals presenting in early infancy with nystagmus, hypotonia, and delayed motor milestones. Brain magnetic resonance imaging demonstrated diffuse hypomyelination, followed by progressive clinical improvement and normalization of myelination on serial imaging. Initial trio whole-exome sequencing was nondiagnostic. Reanalysis-prompted by recognition of additional affected relatives and refinement of human phenotype ontology (HPO) annotation-identified a novel heterozygous TMEM63A variant (c.146G>T; p.Gly49Val). The variant segregated with disease in multiple affected family members.

CONCLUSION

This familial series expands the clinical and genetic spectrum of TMEM63A-related HLD-19. It emphasizes that whole-exome sequencing reanalysis-particularly when family structure or phenotype evolves and when broader HPO terms are applied-can secure a diagnosis and improve counseling and prognostic guidance.

Key Words: Incomplete penetrance; Hypomyelinating leukodystrophy type 19; Hypomyelinating leukodystrophy; TMEM63A; Transient hypomyelination; Case report

Core Tip: Practice-changing diagnostic lesson: In children with early-onset nystagmus, hypotonia, and developmental delay-including hypomyelination syndrome-should be considered. When whole-exome sequencing is nondiagnostic, the appearance of new affected relatives or evolving new phenotype should trigger reanalysis using broader, iteratively refined human phenotype ontology terms, integrated with the suspected inheritance pattern. This strategy improves variant interpretation, increases diagnostic yield, and can ultimately end the diagnostic odyssey.

INTRODUCTION

Hypomyelinating leukodystrophies (HLDs) are a group of rare hereditary disorders characterized by impaired myelin development. Most patients present with hypotonia, nystagmus, ataxia, and developmental delay[1]. Brain magnetic resonance imaging (MRI) is a key diagnostic tool for HLDs, and certain findings may provide clues to genetic etiology, such as atrophy of the putamen and caudate nucleus in TUBB4A-related HLD[2-4].

An increasing number of genes have been linked to HLDs, including PLP1, GJC2, GLB1, TUBB4A, POLR3A, POLR1C, HEXA, and HEXB[5]. The causal genes are involved not only in the production of structural myelin proteins but also in RNA translation and lysosomal protein function[4]. While most HLDs follow an autosomal recessive inheritance pattern, some are X-linked (PLP1) or autosomal dominant (TUBB4A and TMEM63A)[2].

Hypomyelinating leukodystrophy type 19 (HLD-19), also termed transient hypomyelination of infancy, is characterized by nystagmus, motor impairments, and hypomyelination on brain imaging. Here, we report 3 related individuals diagnosed and followed at Siriraj Hospital in whom reanalysis of previously nondiagnostic whole-exome sequencing (WES) identified a novel TMEM63A variant, establishing the diagnosis of HLD-19. We also review and compare their phenotypes to previously reported cases and highlight the importance of WES reanalysis, particularly when new affected family members are identified or when new phenotypic features emerge.

CASE PRESENTATION

Chief complaints

Three related children presented with early-onset horizontal nystagmus and hypotonia with delayed motor milestones.

Case 1 (III-2): A 6-year-old girl was referred to our hospital at 3 months of age because of delayed motor development and hypotonia.

Case 2 (III-3): A 4-year-old girl, a cousin of individual III-2, presented with horizontal nystagmus and head titubation noted in early infancy.

Case 3 (III-4): A 16-month-old boy presented with nystagmus and hypotonia at 2 months of age.

History of present illness

Case 1 (III-2): From 2 weeks of age, she developed horizontal nystagmus, head titubation, and generalized hypotonia. At 3 months, she was unable to support her head, visually track objects, or roll over, but responded to sounds and vocalized.

Case 2 (III-3): At 20 days, her parents noticed horizontal nystagmus and head titubation, initially labeled as congenital nystagmus. At 4 months, she had not achieved head control but could visually track and occasionally reach for nearby objects.

Case 3 (III-4): He developed horizontal nystagmus at 2 months, followed by hypotonia and poor head control, with persistent gross motor delay at 5 months.

History of past illness

All 3 children had unremarkable perinatal and medical histories prior to the onset of symptoms.

Personal and family history

Case 1 (III-2) and Case 2 (III-3): At the initial evaluation of individual III-2, her parents denied a family history of neurologic disorders. After identification of the familial TMEM63A variant, re-interview revealed that the maternal grandmother (I-2) and mother (II-2) had experienced nystagmus and hypotonia during infancy, whereas the mother of Case 2 (II-3) denied similar symptoms.

Case 3 (III-4): He is the younger brother of Case 2 (III-3).

Physical examination

Case 1 (III-2): Neurological examination at 3 months revealed horizontal nystagmus and generalized hypotonia.

Case 2 (III-3): Neurological evaluation at 4 months showed head lag and generalized hypotonia.

Case 3 (III-4): Neurological evaluation at 2 months showed nystagmus along with hypotonia and poor head control.

Laboratory examinations

Case 1 (III-2): Chromosomal analysis and a spastic paraplegia gene panel-including several HLD-related genes such as GJC2-were negative, as a leukodystrophy-specific panel was not available. In 2019, trio WES was reported as negative; at that time.

Case 2 (III-3): After presented with a similar phenotype to Case 1 (III-2)-nystagmus, hypotonia, and motor delay-we reanalyzed the WES data from Case 1 (III-2). Given the pattern of affected cousins across generations, autosomal dominant inheritance with possible incomplete penetrance was suspected. Filtering using the human phenotype ontology (HPO) term “central nervous system hypomyelination” (HP: 0003429) under an autosomal dominant model did not identify a causative gene; however, when we applied the broader term “leukodystrophy” (HP: 0002415), we identified a heterozygous TMEM63A variant, c.146G>T.

Sanger sequencing confirmed the TMEM63A variant in individuals III-2, III-3, and III-4, as well as in their mothers (II-2, II-3) and grandmother (I-2; Figure 1).

Figure 1 Sanger sequencing electropherograms demonstrating segregation of the novel TMEM63A variant in the family. Electropherograms showing the heterozygous TMEM63A c.146G>T (p.Gly49Val) variant identified in affected individuals (III-2, III-3, III-4) and carrier relatives (I-2, II-2, II-3). The arrow indicates the position of the nucleotide substitution. Wild-type sequence is shown for comparison. The color version of this figure is available in the online edition. c: Coding DNA sequence position; p: Protein sequence position; WT: Wild type.

Variant classification

The TMEM63A c.146G>T variant is classified as likely pathogenic according to the American College of Medical Genetics and Genomics guidelines. This classification is supported by the following criteria: PM2, as the variant is absent from population databases; PP1_moderate, due to segregation with disease in 5 affected individuals and 1 asymptomatic carrier; PP3, based on computational predictions suggesting a damaging effect, with SIFT predicting the variant to be deleterious and an Alpha Missense score of 0.96; PP4, given that the clinical phenotype and family history are highly specific for HLDs.

Imaging examinations

Case 1 (III-2): Brain MRI in early infancy suggested hypomyelination (Figure 2A). Follow-up brain MRI at 17, 40 months of age demonstrated age-appropriate myelination (Figure 2B and C).

Figure 2 Serial brain magnetic resonance imaging of individuals III-2 and III-3 demonstrating resolution of hypomyelination. A-E: Axial T2-weighted images of individual III-2 at 3 months (A), 17 months (B), and 40 months (C) of age, and of individual III-3 at 4 months (D) and 15 months (E) of age. Initial images (A and D) demonstrate diffuse T2 hyperintensity of the cerebral white matter consistent with hypomyelination. Follow-up imaging (B, C, and E) shows progressive normalization of white matter signal intensity, indicating age-appropriate myelination.

Case 2 (III-3): Brain MRI in early infancy suggested hypomyelination at 4 months (Figure 2D). Follow-up brain MRI at 15 months of age showed normalized myelination (Figure 2E).

Case 3 (III-4): Brain MRI was not performed.

FINAL DIAGNOSIS

TMEM63A-related HLD-19.

TREATMENT

All 3 children were referred to an early-intervention program with regular physical and occupational therapy focusing on head control, truncal stability, and gross motor skills.

OUTCOME AND FOLLOW-UP

Case 1 (III-2)

Nystagmus gradually improved and resolved by 24 months of age. She achieved head control at 5 months, sat independently at 12 months, and walked alone at 17 months. At the most recent follow-up, her motor function and overall development were age-appropriate, although she had persistent esotropia.

Case 2 (III-3)

Nystagmus resolved earlier, by 15 months of age. She attained head control at 6 months, sat independently at 11 months, and walked alone at 16 months. Her neurological examination and developmental profile are currently normal, with residual esotropia as the only comorbidity.

Case 3 (III-4)

His gross motor milestones have progressed; he achieved head control at 5 months, sat independently at 9 months, and walked alone at 14 months. No other neurological comorbidities have been identified to date.

All 3 adults (I-2, II-2, and II-3) completed higher education and have normal intellectual function.

DISCUSSION

We initially suspected HLDs based on the clinical manifestations of the index patient, including nystagmus, head titubation, hypotonia, and hypomyelination detected by MRI. Most patients with HLDs have unfavorable prognoses due to motor and cognitive impairments. In contrast, the developmental trajectory of HLD-19 improves over time. Reanalysis of trio WES revealed the TMEM63A variant, which explains the patients’ clinical features.

In this case series, we report 3 related individuals diagnosed with HLD-19, a rare form of hypomyelinating leukodystrophy caused by a novel TMEM63A mutation. Our findings underscore the importance of considering autosomal dominant causes of HLDs, particularly in patients presenting with early-onset nystagmus, hypotonia, and delayed motor milestones. Notably, all affected individuals in our study showed developmental improvement and normalization of myelination on follow-up MRI, which distinguishes HLD-19 from other forms of HLDs with more severe and static outcomes. This study also highlights the clinical utility of WES reanalysis, especially in the context of evolving phenotypes or the identification of additional affected family members.

The TMEM63A gene is highly expressed in myelinating oligodendrocytes and microglia[6]; however, the pathophysiological mechanism underlying TMEM63A-related HLD-19 remains unclear. To date, only 8 cases of HLD-19 have been reported in the literature. A summary of their clinical manifestations is presented in Table 1[6-10]. Onset typically occurs in the neonatal period and can resemble Pelizaeus-Merzbacher disease or Pelizaeus-Merzbacher-like disease. Nystagmus often resolves after the first year, though it can persist into later childhood. Development is initially delayed but can normalize over time. Associated features include seizures, myopia, esotropia, learning disabilities, and optic atrophy. However, the disease spectrum can range from mild to severe, with some individuals exhibiting profound developmental delays as reported in prior studies[7,8].

Table 1 Clinical and genetic characteristics of individuals with TMEM63A variants: Present series and published cases.

Individual	Present series			Yan et al[6], 2019				Tonduti et al[7], 2021	Fukumura et al[8], 2022	Gerik-Celebi et al[9], 2023	Siori et al[10], 2024
	Case 1 (III-2)	Case 2 (III-3)	Case 3 (III-4)	Case 1	Case 2	Case 3	Case 4
Sex	Female	Female	Male	Male	Male	Female	Male	Female	Female	Female	Male
Ethnicity	Asian	Asian	Asian	Caucasian	Caucasian	Asian	Asian	Caucasian	Asian	Caucasian	Caucasian
TMEM63A variant (NM_014698.3)	c.146G>T, p.Gly49Val	c.146G>T, p.Gly49Val	c.146G>T, p.Gly49Val	c.1699G>A, p.Gly567Ser	c.1699G>A, p.Gly567Ser	c.1385T>A, p.Ile462Asn	c.503G>A, p.Gly168Glu	c.1675T>C, p.Tyr559His	c.1658G>T, p.Gly553Val	c.33-2A>G, p.?	c.220A>T, p.Arg74*
Inheritance	Maternal	Maternal	Maternal	De novo	Paternal	De novo	De novo	De novo	De novo	Paternal	Paternal
Age at symptom onset	2 weeks	20 days	2 months	2 weeks	1 day	10 days	1 day	1 day	1 day	NA	NA
Nystagmus	+	+	+	+	+	+	+	+	+	+	NA
Resolved at	24 months	15 months	8 months	5 years	7 years	12 months	14 months	NA	NA	NA	NA
Head titubation	+	+	+	+	+	+	+	+	+	NA	NA
Hypotonia	+	+	+	+	+	+	+	+	+	+	+
Ataxia	+	-	-	+	+	-	-	NA	NA	NA	NA
Developmental delay	Age-appropriate	Age-appropriate	Age-appropriate	Age-appropriate	Slight language delay	Age-appropriate	Language delay	Delay at last visit (13 months)	Severe delay	Delay	Delay
Other comorbidities	Esotropia	Esotropia	-	Optic atrophy, myopia, Crohn disease	Seizure, LD, mild myopia, PDA, hypospadias	-	Myopia	Paroxysmal eyelid twitching, spinal cord involvement	Seizure	Dysmorphic facial feature	Dysmorphic facial feature
Motor milestones
Head control	5 months	6 months	5 months	NA	NA	NA	10 months	13 months	Unable	NA	6 months
Sit alone	12 months	11 months	9 months	12 months	NA	NA	16 months	NA	Unable	NA	10 months
Walk alone	17 months	16 months	14 months	20 months	17 months	26 months	36 months	NA	Unable	NA	18 months
Neurophysiological findings	Abnormal ABR/ASSR at 4 months	Normal ABR/ASSR at 1 year	NA	-	Abnormal BAEP, VEP	-	Abnormal BAEP, VEP	Abnormal VEP	Abnormal BAEP	-	-

Data are presented for all individuals with confirmed TMEM63A variants reported in the literature. Plus sign (+) indicates feature present; em dash (-) indicates feature absent or not reported. Motor milestones represent age at achievement. Neurophysiological findings were obtained at varying ages across studies. ABR: Auditory brainstem response; ASSR: Auditory steady-state response; BAEP: Brainstem auditory evoked potential; LD: Learning disability; NA: Not available; PDA: Patent ductus arteriosus; VEP: Visual evoked potential.

Individual II-3, who is unaffected despite carrying the mutation, suggests incomplete penetrance in HLD-19. While the exact penetrance rate is unknown, similar findings have been reported in the literature[6,10]. Therefore, future studies involving larger populations are needed to better understand disease penetrance and variability.

The diagnostic yield of WES for rare diseases is approximately 30%[11], although this can vary depending on the phenotype. Whole-exome sequencing may be nondiagnostic for several reasons. Technical limitations such as incomplete coverage, structural variants/copy number variants, mosaicism, and intronic/regulatory variants-may prevent variant detection[12]. Knowledge limitations at the time of interpretation also play a role, as gene-disease associations and variant databases continually evolve. Additionally, phenotype-driven filtering limitations may arise when overly narrow clinical descriptors unintentionally exclude the true causal gene. In disorders with incomplete penetrance, inherited variants may be deprioritized when the transmitting parent is apparently unaffected, further increasing the risk of a false-negative interpretation.

In the present family, reanalysis triggered by identification of an additional affected relative, together with adjustment of phenotype annotation, proved crucial. Filtering with a narrow HPO term (such as “central nervous system hypomyelination”) did not reveal a candidate. However, applying a broader HPO term (“leukodystrophy”) enabled identification of the causal TMEM63A variant. These observations support periodic WES reanalysis-especially when new family members become affected or clinical features evolve-and emphasize the practical value of iterative HPO term selection to improve diagnostic yield.

CONCLUSION

This familial series expands the genotypic and phenotypic spectrum of TMEM63A-related HLD-19 and supports considering autosomal dominant causes in infants with nystagmus, hypotonia, and hypomyelination. Developmental catch-up with improved myelination on follow-up MRI favors HLD-19. Our findings provide new evidence that HLD-19 may show incomplete penetrance, which is important for interpretation and counseling. Periodic WES reanalysis-especially when additional affected relatives are identified or the phenotype evolves-can end the diagnostic journey by securing a molecular diagnosis and enabling timely counseling.

ACKNOWLEDGEMENTS

We extend our gratitude to Mrs Maneewan Ladee for her valuable contribution. We are also indebted to Mr David Park for the English-language editing of this paper. Most importantly, we sincerely thank all the children and families who participated in this study for their invaluable contribution.