Novel nonsense mutation in the TCOF1 gene associated with treacher collins syndrome: A case report

Abstract

Treacher Collins Syndrome (TCS) is a congenital disorder characterized by craniofacial malformations. In this case, a novel likely pathogenic nonsense variant, in the TCOF1 gene, associated with TCS, was reported. Genetic analysis was performed on an Ecuadorian participant (Subject A) and his mother (Subject B), both of whom exhibited characteristic features of TCS. Next-generation sequencing (NGS) identified a single nucleotide variant (c.4423A > T) in exon 25 of the TCOF1 gene, resulting in a premature stop codon (p.(Lys1475Ter)) and a truncated treacle protein. The likely pathogenic variant presented in Subjects A and B could alter critical functions of the protein, contributing to the craniofacial malformations of the subjects. The variant informed in this case report contributes to the knowledge of TCOF1 gene variants associated with TCS and highlights the importance of genomic screening for accurate diagnosis and improved clinical management in patients and families.

Introduction

Treacher Collins Syndrome (TCS) is a rare congenital disorder characterized by craniofacial dysmorphism. ¹ TCS is associated with variants in the TCOF1, POLR1B, POLR1C, and POLR1D genes, with the type of TCS varies depending on the affected gene.^2,3

Most TCS cases are caused by alterations in the TCOF1 gene, following an autosomal dominant hereditary pattern. The TCOF1 gene plays a key role in various crucial cellular processes, including mitosis regulation, ribosome biogenesis, ubiquitination, response to DNA damage, and telomere integrity. ⁴

To date, no studies have reported the prevalence or genomic characteristics of TCS in Ecuador. Thus, we present the first genomic data from an Ecuadorian patient clinically diagnosed with TCS. Furthermore, the likely pathogenic variant described in this article has not been previously described. This study adheres to CARE guidelines. ⁵

Case description

Familial history

Subject A is a newborn Ecuadorian male delivered via cesarean section at Hospital Enrique Garcés in Quito, Ecuador, in December 2022. At birth, the medical team observed dysmorphic facial features, including a downward slant of the palpebral fissures, ptosis of the upper eyelids, retrognathia, lower eyelid pseudocolobomas, low-set ears, hypoplastic cheekbones, and ankyloglossia (Figure 1A-B). Additionally, the infant failed bilateral auditory screening tests.

Figure 1.

A: Maxillofacial malformations of subject A at birth. A downward slant of the palpebral fissures, ptosis of the upper eyelids, retrognathia, lower eyelid pseudocolobomas, low-set ears, and hypoplastic cheekbones can be observed; B: Craniofacial dysmorphism of subject A at 15 days old; C: Phenotypic comparison between subject A and TCS composite photo. Areas in red and yellow indicate regions with high similarity. Image was generated using the software Face2Gene.

Moreover, a composite photo was created using the Face2Gene software ⁶ under pre-established parameters to determine a possible diagnostic based on the phenotypic features. The analyses revealed a high phenotypic similarity to TCS (Figure 1C).

A family tree was reconstructed based on information provided by the proband's mother (Subject B). During the reconstruction of the family tree, subject B mentioned that her father exhibited two phenotypic features associated with TCS: downward-slanting palpebral fissures and ptosis of the upper eyelids. However, he was never diagnosed with a genetic disorder and declined to undergo genomic testing (Figure 2).

Figure 2.

Family pedigree of subjects A and B.

We observed that Subject B exhibits phenotypic characteristics compatible with TCS; however, she has not been diagnosed and does not recognize her facial features as suggestive of TCS. Therefore, she was invited to participate in the study to determine if she carries the same variant as her son. A timeline summarizing relevant data from the care episodes has been included in Figure 3.

Figure 3.

Timeline displaying the relevant clinical events for both subjects.

Genetic results

Next-generation sequencing (NGS) is performed using the TruSight One (TSO) kit (Illumina) and processed according to the manufacturer's protocol. The genomic data analysis was carried out utilizing the reference genome (hg38), DRAGEN Enrichment v. 3.9.5, Variant Interpreter v.2.16.1.300, PolyPhen, and Sift. The results for both Subject A and Subject B revealed a novel, unreported nonsense variant in heterozygosity (NM_001135243.1: c.4423A > T, p.(Lys1475Ter)) in the TCOF1 gene. This variant is predicted to be likely pathogenic. The sequencing data have been deposited in the Sequence Read Archive (SRA) data available in the NCBI database under accession numbers SRX27811870 and SRX27811871 for subject A and B, respectively; whereas the SNP variant ID is available under the SUB15175176 number.

Furthermore, PCR was performed using 46 Ancestry Informative Markers (AIMs) based on the method described by Zambrano AK. et al. (2019). ⁷ Ancestral inference analysis was performed with STRUCTURE v.2.3.4 software for an admixture model.

Ancestry composition analysis revealed that Subject A was 18.4% African, 39.8% European, and 41.8% Native American, while Subject B was 11.1% African, 18.3% European, and 70.6% Native American, respectively.

Discussion

TCS1 is an autosomal dominant disease characterized by congenital craniofacial dysplasia.^8,9 Subjects A and B harbor a novel heterozygous likely pathogenic nonsense variant c.4423A > T in the TCOF1 gene. However, these individuals exhibit different TCS phenotypes. Subject A displayed the most common phenotypic characteristic of TCS at birth (Figure 1A), while Subject B had only mild craniofacial dysplasia. Another notable difference was subject A's failed bilateral auditory screening test, whereas subject B didn’t show hearing loss symptoms. Congenital hearing loss is frequently reported in TCS1 cases.^9,10

The set of phenotypic characteristics in subject A, and the mildly affected phenotype of subject B, shows the heterogeneous clinical presentation of this syndrome.^9,11 These effects have also been described in previous research. ¹²

In the present study, a novel variant (c.4423A > T) in the TCOF1 gene was identified in both individuals. The variant leads to a premature termination codon at position p. (Lys1475Ter), resulting in a truncated protein. A premature stop codon in the last exons has been associated with a more severe phenotype.^9,11

This study reports a likely pathogenic variant in exon 25/27, a region critical for the nuclear localization signal (NLS). ¹³ Alterations in the NLS domain, induced by pathogenic variants in exon 25, may disrupt key processes such as ribosomal biogenesis and neural crest cell development, essential for craniofacial differentiation. ¹⁴

The more severe symptoms in subject A could be partially explained by nonsense-mediated mRNA decay (NMD), which may degrade the truncated TCOF1 transcript, leading to a lower treacle protein expression during embryonic development. ¹⁵ Some studies have proposed that the inhibition of NMD could enhance the levels of transcripts containing nonsense variants. ¹⁶ Therefore, this therapeutic approach could be assessed in embryonic animal models harboring TCOF1 stop-gain variants to assess its potential for reducing NMD activity, contributing to the decrease of severe TCS symptoms.

The ancestry composition of these individuals showed notable differences. Subject's A ancestry was predominantly European (39.8%) and Native American (41.8%), whereas Subject's B ancestry is primarily Native American (70.6%). Although TCS cases have been described in diverse populations, no studies have established a higher prevalence in specific ethnic groups.^17–19

Approximately 40% of TCS cases are familial, while 60% may be attributable to de novo pathogenic variants. ²⁰ Thus, all TCS patients and their families should undergo genetic analysis to establish if the condition is inherited or results from a spontaneous mutation. Unfortunately, genetic testing and comprehensive prenatal screening remain rare in affected families.

Children with TCS often undergo years of medical visits before receiving a diagnosis, as distinguishing TCS from phenotypically similar disorders, such as Goldenhar syndrome, can be challenging. ³ Genomic testing plays a crucial role in the diagnosis and management of genetic diseases like TCS. Early identification of the genetic variant allows for an accurate diagnosis and differentiation from other craniofacial disorders. Although the majority of TCS cases are due to TCOF1 variants, accurate variant identification is vital for timely interventions. ²¹

Conclusions

This case report describes a novel likely pathogenic variant in the TCOF1 gene, c.4423A > T, associated with TCS. It is the first study to report this variant in two individuals from an Ecuadorian family. The phenotypic variability observed, particularly in Subject B, who exhibited mild traits without significant health problems, underlines the variable expressivity of TCS. This case exemplifies the importance of genetic testing by NGS in the diagnosis and management of inherited diseases. Furthermore, the integration of genetics into clinical practice is a crucial step towards a more effective and personalized diagnosis for the benefit of patients and their families.