Undiagnosed Diseases Program

National Human Genome Research Institute

Investigators

Linked publications & trials

Abstract

1. The NIH Undiagnosed Diseases Program (UDP) is supported by an IC Directors’ school tax. William Gahl, MD, PhD, and David Adams, MD, PhD, co-direct the UDP; Cynthia Tifft, MD, PhD, runs the Pediatric UDP; May Malicdan, MD, PhD, manages the UDP’s Translational Research Program; and Camilo Toro, MD, directs the adult portion of the UDP. Dr. Toro and Maria Acosta, MD, are UDP neurologists, Donna Novacic, MD, is an internist, and Francis Rossignol, MD, is an internist and clinical and biochemical geneticist; Lynne Wolfe, NP, is the UDP Site Coordinator. In FY25, the UDP reviewed 222 applications; 41 patients were evaluated and 13 more are scheduled in FY25. Ten patients were transferred from closed UDN clinical sites. One-third of patients evaluated are pediatric. The UDP also followed up on numerous previous patients and responded to scores of inquiries. 2. In FY25, UDP investigators and collaborators diagnosed several very rare diseases. These included the clinical disorders associated with variants in ZFX, EHMT2, SLC4A1, EIF2AK2, PDGFB, SPTAN1, ATG4D, RFC4, YPEL3, SETD5, TEMPI, AMPD1, RFC1, and KIF11. Dr. Adams and Lynne Wolfe diagnosed a patient with a pathogenic variant in UQCRFS causing mitochondrial complex III deficiency with lactic acidosis and scalp alopecia. Remarkably, the patient also had a GJA8 variant causing cataracts. The neurology team of Dr. Acosta described a low-grade glioma growing for a decade in an adolescent boy. In another case, RNAseq revealed a deep intronic deletion causing abnormal splicing in the trifunctional protein gene, making the diagnosis of this mitochondrial disorder. RNAseq was also employed by UDP bioinformaticians to detect a deep intronic variant in NBAS, whose gene product functions in retrograde transport (Golgi to ER) and in nonsense-mediated decay. The patient’s development delay, impaired growth, facial dysmorphisms, osteopenia, and ocular abnormalities expand the phenotype of NBAS deficiency. Dr. Toro previously diagnosed a patient with biallelic AFG3L2 variants causing spastic ataxia type 5, with cerebellar ataxia, spasticity, dystonia, and myoclonic epilepsy. He and his collaborators found that absence of AFG3L2, a mitochondrial protease, causes accumulation of proteins that elicit an overactive but protective stress response mediated by the protease OMA1. Dr. Toro also coauthored articles describing a frontotemporal lobar degeneration tauopathy associated with VCP D395G, a lamin B1 silencer element in oligodendrocytes causing Autosomal Dominant Leukodystrophy, and cases of cerebellar ataxia due to monoallelic RAB3A variants. 3. The UDP described several new genetic diseases. Marie Morimoto, PhD, and Dr. Malicdan discovered a new disease that was named after them. Morimoto-Ryu-Malicdan Neuromuscular Syndrome was found to affect 9 individuals with poor coordination, muscle weakness, hearing deficits, and decreased body weight due to deficiency of RFC4, a component of Replication Factor C. This protein complex enhances DNA polymerase processivity for recruiting replication factors and repair proteins. Drs. Morimoto and Malicdan used in silico studies and structural, cellular, and functional analyses to demonstrate the new disease-gene association. UDP members also coauthored a Nature article that included UDP patients with neurodevelopmental delay due to de novo variants in RNU4-2 snRNA. This new disorder does not involve mutations in a protein-encoding gene. Rather, RNU4-2 encodes a small nuclear RNA (U4) that is part of a tri-snRNP complex critical for splicing. RNU4-2 is extensively expressed in the brain during development; its deficiency disrupts a 5’ splice site, resulting in impaired neurodevelopment. Dr. Toro also contributed to a consortium that identified pathogenic SRPK3 variants in 9 individuals with X-linked intellectual disability (XLID) from 5 different families. The patients had agenesis of the corpus callosum, ataxia, and abnormal eye movements, defining a new genetic subset of XLID patients. The group also created a zebrafish model mimicking the human disorder. Another new genetic disease discovered by UDP investigators and their collaborators involves WASHC3. Three individuals with either a dominant negative variant or homozygous pathogenic variants in WASHC3 presented with facial dysmorphisms, development delays, and short stature. The WASH protein complex promotes parathyroid hormone receptor (PTH1R) trafficking; WASH deficiency diminishes PTH1R signaling and impairs growth plate chondrocyte differentiation. Dr. Malicdan helped identify a new disorder of lysophospholipid transport due to SPNS1 variants. Finally, the UDP Translational Research group described a patient with dysmorphisms, ichthyosis, and bone dysplasia associated with compound heterozygous, pathogenic variants in DDX41 (DEAD-box helicase 41). This gene functions in innate immunity by regulating RNA metabolism; it senses viral DNA and activates interferon signaling via the STING-TBK1-IRF3 pathway. Prashant Sharma, PhD, and Dr. Malicdan led a group that demonstrated dysfunction of interferon pathway genes and upregulation of periostin expression, explaining the skeletal abnormalities. 4. In FY25, the UDP expounded on its approach to undiagnosed disorders. Dr. Adams wrote a book chapter on the subject for Harrison’s Principles of Internal Medicine and an article as a member of the Diagnostic Scientific Committee for the International Rare Disease Research Consortium (IRDIRC). Other UDP staff, led by Dr. Tifft, described methodologies for genotyping and phenotyping of pediatric UDP patients. Several UDP and UDN investigators reported their effective use of telehealth for undiagnosed individuals, and the pediatric UDP group wrote an editorial on CNS imaging in rare disease diagnosis. Dr. Gahl helped describe the international challenges of pursing rare disease research and care. Drs. Adams and Toro contributed to an article on detecting repeat expansions in new human disorders. Dr. Malicdan contributed to descriptions of a Rothmund-Thomson Syndrome patient diagnosed by an Undiagnosed Hackathon and to an article on tandem acceptor splice sites in human disease. 5. The UDP expanded its analytical repertoire to develop bioinformatics analysis tools, including improved SNP visualization, genomics, RNASeq and long read sequence data. Our CNV and structural variant pipeline now shows QA and cohort comparison data, allowing rapid validation of cohort outliers, mosaicism and uniparental disomy. A UDP shared PhD student Sarah Silverstein continued to develop an optimized software ensemble pipeline for RNASeq analysis with improved sensitivity and specificity for true disease-associated splice events. The UDP bioinformatics core continues to support collaborative clinical and translational bioinformatics tool development. Drs. Tifft and Adams helped create a new tool, LUSTR, to call genome-wide germline and somatic short tandem repeat variants. Ongoing collaboration with the Miller laboratory at the University of Washington explores the use of long-read sequencing to phase compound heterozygous variants in individuals lacking parental genomic samples. These projects have yielded new diagnostic candidates. 6. In FY25, the UDP mentored 10 postbacc IRTAs and helped train two predoctoral students and several NHGRI genetics fellows. Dr. Adams directs a Bioinformatic Journal Club and Dr. Gahl conducts weekly UDP patient rounds for 50-70 IRTAs and others. Gahl is PI of the UDN’s clinical protocol, 15-HG-0130 “Clinical and Genetic Evaluation of Patients with Undiagnosed Disorders Through the Undiagnosed Diseases Network”. Drs. Gahl, Toro and Adams serve on the UDN Executive Committee. Dr. Toro serves on the UDN Steering Committee; Adams is on the Clinical and Tool Building Working Group and the Therapeutic Matching Committee; Dr. Malicdan co-chairs the Model Organisms Committee; and Lynne Wolfe chairs the Site Operations Committee. The UDP also contributed to 24 articles published by the UDN in FY25 and that are not listed in the bibliography of this report. 7. Dr. Gahl leads the Undiagnosed Diseases Network International (UDNI), consisting of >200 physicians and scientists from 60 nations. Dr. Adams chairs the UDNI’s Data Sharing and Technology Working Group. Scores of UDPs now exist around the world. Gahl is currently coordinating the 14th UDNI conference in Rio de Janeiro and supporting the UDNI’s Champions Initiative to foster UDPs in low and middle income countries. UDP members delivered numerous national and international presentations on the Program.