Rare Disease

Advancing Understanding
of Rare Disease

Annually, up to 10 percent of the nearly 4 million babies born in the US are hospitalized in an intensive care unit due to an underlying rare genetic disease. Without proper diagnosis and treatment, some such disorders can lead to permanent disability or even death.

Many rare genetic diseases are never seen by most physicians, as they affect very few children worldwide. This creates challenges in recognizing the condition and knowing how to treat it.

At RCIGM, we want to provide accurate information when a rare disorder is diagnosed to enable families and their healthcare teams to make informed decisions about treatment. 

Knowledge Generation

  • We identify new diseases.
  • We study the normal disease progression of the rare diseases we diagnose.
  • We evaluate treatments for rare disease, including trying medicines not previously used in children, and participating in research with drug companies to evaluate the efficacy of potential new therapies.

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Key Facts

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Publications

Genet Med. 2026 Oct 27:102776. doi: 10.1016/j.gim.2026.102776. Online ahead of print.

ABSTRACT

PURPOSE: While heterozygous de novo missense variants in the microtubule-binding GAR domain of Microtubule-actin cross-linking factor 1 (MACF1) cause Lissencephaly 9 with Complex Brainstem Malformations (LIS9) [MIM 618325], the phenotypic impact of variants outside this domain remains unclear.

METHODS: We assembled a cohort of 5 affected individuals from 4 unrelated families with biallelic non-GAR domain MACF1 variants who exhibit partially overlapping yet unique phenotypic traits. A sixth individual with a de novo, heterozygous frameshift variant was additionally identified. Combined with previously reported cases, we analyzed genotype and phenotype data from 22 individuals using Human Phenotype Ontology (HPO)-based unsupervised hierarchical clustering.

RESULTS: Clustering revealed two distinct phenotypic signatures, suggesting domain-associated effects. Variants outside the GAR domain associate with broader neurodevelopmental phenotypes and craniofacial and skeletal involvement. Enrichment analysis (p < 0.001) using OMIM HPO sets supported these findings. In contrast to the GAR domain’s strong correlation with LIS9, biallelic non-GAR domain MACF1 variants were linked to distinct developmental anomalies.

CONCLUSION: These results expand the phenotypic spectrum of MACF1-related disorders and provide preliminary evidence for domain-associated MACF1 variant effects. While limited by sample size and lack of functional validation, these findings should be considered hypothesis-generating and underscore the utility of HPO-based clustering for systematic phenotype comparison as additional cases emerge. Comprehensive genetic and phenotypic assessments are essential for understanding the role of MACF1 in development, informing diagnosis, and guiding future research on cytoskeletal regulation in neurodevelopment.

PMID:42937053 | DOI:10.1016/j.gim.2026.102776

Nucleic Acids Res. 2026 May 20;54(10):gkag504. doi: 10.1093/nar/gkag504.

ABSTRACT

Patients with extremely rare pathogenic variants pose unique challenges to current healthcare systems. Nano-rare mutations have been defined as mutations with a known prevalence of <30 patients worldwide, but because of the small fraction of humans who have undergone genetic testing, neither the precise prevalence of individual mutations nor the total prevalence of patients with nano-rare mutations is known. n-Lorem is a non-profit founded in 2020 with the mission of equitably discovering, developing, and providing bespoke experimental antisense oligonucleotides (ASOs) for free, for life, to patients with nano-rare mutations that are amenable to ASO treatment. In this perspective, we provide an overview of the n-Lorem processes and systems, the characteristics of the first 329 patients who have applied for treatment for whom initial assessment was completed and suitability for ASO treatment determined, and a summary of the results of ASO treatment for patients treated to date. Detailed data on individual patients and the overall clinical safety and tolerability profiles of the ASOs for which there are clinical data are the subjects of other manuscripts.

PMID:42227334 | DOI:10.1093/nar/gkag504

Nat Commun. 2025 Aug 7;16(1):7267. doi: 10.1038/s41467-025-61712-2.

ABSTRACT

Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform in-depth analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development. The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale case-based diagnostic analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser ( https://dbmi-bgm.github.io/udn-browser/ ). These results show that case-level diagnostic efforts should be supplemented by a joint genomic analysis across cohorts.

PMID:40770127 | DOI:10.1038/s41467-025-61712-2

Nature. 2025 Mar 26. doi: 10.1038/s41586-025-08676-x. Online ahead of print.

ABSTRACT

Meningomyelocele (also known as spina bifida) is considered to be a genetically complex disease resulting from a failure of the neural tube to close. Individuals with meningomyelocele display neuromotor disability and frequent hydrocephalus, requiring ventricular shunting. A few genes have been proposed to contribute to disease susceptibility, but beyond that it remains unexplained1. We postulated that de novo mutations under purifying selection contribute to the risk of developing meningomyelocele2. Here we recruited a cohort of 851 meningomyelocele trios who required shunting at birth and 732 control trios, and found that de novo likely gene disruption or damaging missense mutations occurred in approximately 22.3% of subjects, with 28% of such variants estimated to contribute to disease risk. The 187 genes with damaging de novo mutations collectively define networks including actin cytoskeleton and microtubule-based processes, Netrin-1 signalling and chromatin-modifying enzymes. Gene validation demonstrated partial or complete loss of function, impaired signalling and defective closure of the neural tube in Xenopus embryos. Our results indicate that de novo mutations make key contributions to meningomyelocele risk, and highlight critical pathways required for neural tube closure in human embryogenesis.

PMID:40140573 | DOI:10.1038/s41586-025-08676-x

Ther Adv Rare Dis. 2024 Jul 31;5:26330040241263972. doi: 10.1177/26330040241263972. eCollection 2024 Jan-Dec.

ABSTRACT

TESS Research Foundation (TESS) is a patient-led nonprofit organization seeking to understand the basic biology and clinical impact of pathogenic variants in the SLC13A5 gene. TESS aims to improve the fundamental understanding of citrate’s role in the brain, and ultimately identify treatments and cures for the associated disease. TESS identifies, organizes, and develops collaboration between researchers, patients, clinicians, and the pharmaceutical industry to improve the lives of those suffering from SLC13A5 citrate transport disorder. TESS and its partners have developed multiple molecular tools, cellular and animal models, and taken the first steps toward drug discovery and development for this disease. However, much remains to be done to improve our understanding of the disorder associated with SLC13A5 variants and identify effective treatments for this devastating disease. Here, we describe the available SLC13A5 resources from the community of experts, to foundational tools, to in vivo and in vitro tools, and discuss unanswered research questions needed to move closer to a cure.

PMID:39091896 | PMC:PMC11292725 | DOI:10.1177/26330040241263972

J Pediatr. 2024 Jul 4:114180. doi: 10.1016/j.jpeds.2024.114180. Online ahead of print.

ABSTRACT

To evaluate a novel candidate disease gene, we engaged international collaborators and identified rare, biallelic, specifically homozygous, loss of function variants in SENP7 in four children from three unrelated families presenting with neurodevelopmental abnormalities, dysmorphism, and immunodeficiency. Their clinical presentations were characterized by hypogammaglobulinemia, intermittent neutropenia, and ultimately death in infancy for all four patients. SENP7 is a sentrin-specific protease involved in posttranslational modification of proteins essential for cell regulation, via a process referred to as deSUMOylation. We propose that deficiency of deSUMOylation may represent a novel mechanism of primary immunodeficiency.

PMID:38972567 | DOI:10.1016/j.jpeds.2024.114180

Knowledge Generation

In Line Title

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In Line Title

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Read more about this groundbreaking work.

Robert Wechler-Reva

PHD, Neuro-Oncology Program Director

Noted scientist Robert Wechsler-Reya, PhD, is also a professor and researcher at the Sanford Burnham Prebys Medical Discovery Institute (SBP) where he is focused on investigating the genes and nervous system signaling pathways that contribute to medulloblastoma, the most common malignant brain tumor in children.

News Features

October 22, 2020

Variety.com

Inside Our Child’s Battle With Mitochondrial Disease

“Despite a beautiful pregnancy and delivery with every prenatal screening and precaution taken, Evan was born with mitochondrial disease.” Lindzi Scharf shares a … Read More

October 14, 2020

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Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent lobortis, est eget hendrerit rutrum, … Read More

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