A global group of researchers has successfully identified the genetic cause of conditions affecting 30 individuals, who had been without a diagnosis for years despite comprehensive testing. This research was done by experts from Baylor College of Medicine, the National University of Singapore, and a variety of international institutions, and published in Genetics in Medicine, the journal of the American College of Medical Genetics and Genomics.
“Our discoveries began with a patient in the clinic who presented with a unique mix of symptoms,” explained Dr. Daniel Calame, the first author and co-corresponding author of the study. He serves as an instructor of pediatric neurology and developmental neurosciences at Baylor. “This patient exhibited serious developmental disorders, epilepsy, and complete insensitivity to pain, which was extremely unusual. Despite extensive evaluations by geneticists and neurologists, a diagnosis remained elusive.”
He enrolled the patient in the BCM GREGoR (Genomics Research to Elucidate the Genetics of Rare Diseases) research program. “Upon reexamining the genetic and clinical data for this patient, we pinpointed a mutation in the gene FLVCR1, leading us to a complex medical mystery,” said Calame.
One gene, multiple issues
To investigate how the rare mutation of FLVCR1 could explain the patient’s condition, Calame and his team delved into existing scientific literature on this particular gene. Evidence suggests that the FLVCR1 protein is crucial for producing red blood cells and for the transport of choline and ethanolamine within cells. These substances are vital for cellular health as they serve as building blocks for phosphatidylcholine and phosphatidylethanolamine, essential for maintaining cell membrane structure, facilitating cell division, and supporting necessary cellular functions.
Other studies have explored the equivalent of the human FLVCR1 gene in animal models. Research showed that when the gene was inactivated in mice, it resulted in death during the embryonic phase. “The embryos displayed various bone deformities in the head and limbs, alongside problems with red blood cell production, symptoms akin to Diamond-Blackfan anemia (DBA) in humans,” Calame noted. “However, this differed significantly from our patient’s condition.”
DBA patients also face skeletal deformities. Interestingly, while the evidence from mouse models suggested that FLVCR1 was linked to DBA, it was not recognized as a contributing factor in DBA patients initially, as other genes had been linked to the disorder.
Moreover, further investigations discovered rare defective versions of the FLVCR1 gene in individuals experiencing childhood or adult-onset ataxia, which is characterized by poor motor control and lack of coordination, alongside sensory issues and retinitis pigmentosa, leading to progressive vision loss. However, these symptoms did not align with what Calame observed in his patient.
“We found this very interesting. On one side, we had a patient with a rare FLVCR1 mutation showing severe developmental troubles, epilepsy, and total insensitivity to pain, while on the other side, patients with different FLVCR1 mutations showed varying issues,” Calame stated. “Could it be possible that different mutations in FLVCR1 resulted in a spectrum of symptoms observed in all the patients together?”
Deciphering the FLVCR1 enigma brings clarity to patients
The researchers took an innovative approach to unraveling this mystery using two strategies. The first strategy involved expanding the patient pool by locating individuals with undiagnosed neurodevelopmental disorders and variants of the FLVCR1 gene from large, specialized datasets. They tracked these individuals through databases such as the Baylor-Hopkins Center for Mendelian Genomics/BCM GREGoR, the Baylor Genetics clinical diagnostic lab, GeneMatcher, and other related research and diagnostic labs.
“We were able to identify 30 patients from 23 unrelated families with rare FLVCR1 variants,” shared Calame.
The team discovered 22 different gene variants, with 20 being previously unreported. The characteristics of these patients varied from severe developmental disorders with major delays, microcephaly (abnormally small head size), brain malformations, epilepsy, and early death. The severely affected patients had shared traits, including anemia and skeleton deformities, aligning them with the mice lacking the Flvcr1 gene and DBA, which had never been linked to FLVCR1 before.
The second strategic approach was to analyze the functional impacts of FLVCR1 variants in laboratory experiments in collaboration with Dr. Long Nam Nguyen and his team from the Yoon Long Lin School of Medicine at the National University of Singapore. The aim was to understand how the different patient variants influenced the transport of choline and ethanolamine within cells in laboratory settings. The results indicated that these FLVCR1 variants significantly reduce the transportation of choline and ethanolamine—up to half that seen with normal FLVCR1 proteins. “We suspect that the severity of the disease directly relates to the residual transport activity of the specific FLVCR1 variants a patient possesses,” Calame explained.
Other studies have pointed out that choline is essential for normal brain development, and a shortage of it can also lead to anemia, liver problems, growth hindrances, and immune deficiencies. “The lack of proper choline uptake disrupts brain development, and we established that the variants in our patients do decrease choline transport,” he added.
Overall, the findings reveal that FLVCR1 variants are responsible for a wide range of developmental issues, extending from severe multiorgan developmental disorders that resemble DBA to adult-onset neurodegenerative conditions. The variants discovered in these patients diminish choline and ethanolamine transport in laboratory tests, indicating that transporting these molecules into the central and peripheral nervous systems is vital to prevent neurodegeneration and necessary for healthy brain development.
“Our results also highlight the need for further exploration of the potential benefits of choline or ethanolamine supplements in treating FLVCR1-related diseases,” Calame pointed out. “The 30 patients identified had spent years without a diagnosis; it was fulfilling to finally offer clarity regarding their conditions.”
This research emphasizes the necessity of taking a comprehensive approach to diagnosing rare diseases. “All 30 severely affected individuals mentioned here had previously undergone extensive clinical or research exome or genome sequencing, which revealed the FLVCR1 variants. However, these variants were often considered either inconsequential or uncertain because of the mismatched symptoms across patients,” Calame noted. “Such misconceptions underscore the importance of integrating findings from model organism studies into personalized genomic analysis for rare diseases, and the need to anticipate both severe and mild characteristics associated with each disease gene to enhance diagnostic genetic testing outcomes.”
