We are presenting the case of a 6-year-old male patient with progeroid phenotype and severe developmental delay referred to Genetic clinic. Given the complex phenotype an extensive metabolic and ...genetic evaluation was performed including a whole exome sequencing analysis that showed genetic variants in
TTR, RELN, MYH6, PHIP
, and
SYNE2
genes. Patients’ mother and brother were analyzed for the genetic variants in
MYH6, PHIP
and
RELN
. Both had same variants on
PHIP
and
RELN
as our patient, with no apparent phenotypical consequences. Physical examination was remarkable for dysmorphism including plagiocephaly, low set and abnormally shaped ears, up slanted palpebral fissures, hypoplastic alae nasi, and a head circumference two standard deviations below the 3
rd
percentile (microcephaly). Other characteristics include wrinkled skin, a broad forehead, sparse eyelashes in lower eyelid, short palpebral fissures, upturned nares, thick lips, right occipital plagiocephaly, overfolded helix and prominent anti-helix, protuberant chest, scaphoid abdomen, digitalized thumbs, and kyphosis due to low muscle tone. The patient presented abnormal EEG with evidence of epileptic discharges. A temporal bone CT showed plagiocephaly with flattening of the right occipital bone. Brain MRI showed callosal agenesis with bilateral colpocephaly with temporal horn dilatation, parahippocampal atrophy, lissencephaly and midbrain hypoplasia. The combination of
de novo
gene variants mentioned above has never been reported nor correlated as the result of haploinsufficiency mechanisms. Thus, we propose haploinsufficiency and loss of heterozygosity as etiological reasons for this patient phenotype. Further proteomic studies are needed to allocate the extense of genetic influence within the clinical manifestations.
OBJECTIVES/GOALS: Assess the diagnostic yield and test utilization of WES in patients having complex traits. We aim to evaluate the use of the first genetic approach for the identification of primary ...variants that contribute to neurogenetic disease etiology and influence onset and progression in Puerto Ricans. METHODS/STUDY POPULATION: Prospective cohort of 45 Puerto Rican probands (19 months - 36 years old) with complex neurogenetic traits that underwent WES (2019 - 2021). WES was performed, including copy number variant analysis and mitochondrial genome sequencing. We evaluated several factors possibly influencing the rate of WES diagnosis including early age, consanguinity, and family history of neurogenetic diseases. In addition, we only evaluated probands rather than dyads/trios and the clinical phenotypes. Descriptive analysis was performed, including a catalog of all variants reported. Multivariate analysis was performed to estimate the statistical association between variants and phenotypes reported and adjusting for potential confounders (age, sex, family history, income, health insurance and zip code). RESULTS/ANTICIPATED RESULTS: Auspiciously, positive pathogenic findings altered the clinical management in 29% of the probands in this study. A likely genetic diagnosis was achieved in 53% of the probands including pathogenic, likely pathogenic and variants of uncertain significance. Intronic variants, copy number variants detection and mitochondrial genome was included in WES methodology. Despite these facts, a 47% of the reported WES were negative, which deserve re-analysis potentially genotype based. Multivariate analysis is expected to adjust for potential confounders to establish a genotype-phenotype correlations in neurogenetic complex traits in this Puerto Rican admixed population. DISCUSSION/SIGNIFICANCE: Clinical WES offers an alternative approach for identification of variants in patients with complex traits. WES is also applicable in genetically heterogeneous individuals when specific genetic tests are not available or unsuccessful. Variants reported contribute to understand complex neurogenetic disease in underrepresented Puerto Ricans.
ABSTRACT IMPACT: Alterations in mitochondrial metabolism affect any tissue, especially those with the highest demand for energy. As the symptoms and clinical manifestations are heterogenous, disease ...diagnosis is challenging. The implementation of genetic-first approach in the diagnosis of mitochondrial diseases will expedite confirmation, treatment, management, and counseling of affected Puerto Rican individuals. OBJECTIVES/GOALS: Mitochondrial diseases are rare, and diagnosis is complex due to the heterogeneity of clinical manifestations. We aim to develop and implement a testing algorithm using a genetics-first approach, facilitating the identification of variants that contribute to mitochondrial disease’s etiology and influence onset and progression in Puerto Ricans. METHODS/STUDY POPULATION: This is a cross-sectional study for characterizing clinical laboratory results from profiles used to evaluate metabolic diseases in individuals with suspected mitochondrial disorders from 2018 to 2021. A subset of 25 individuals from biochemical profile will be recruited to analyze their medical and family history, metabolic biomarkers in blood and urine, hearing test, imaging and chromosomal microarray. The implementation of a genetic testing algorithm using whole exome and mitochondrial DNA sequencing will be performed in a subset of 11 randomized individuals. Descriptive analysis will be reported, including a catalog of all variants. Multivariate analysis will be performed to estimate the statistical association between variants and phenotypes reported and adjusting for potential confounders. RESULTS/ANTICIPATED RESULTS: The biochemical profile of pediatric Puerto Rican individuals suspected of having mitochondrial diseases will be altered and can be used to differentiate among other metabolic causes. We expect to find altered levels of lactate, pyruvate and carnitines in serum, as well as altered organic acids in urine. The implementation of a testing algorithm using both, mitochondrial DNA and whole exome sequencing as first approach will be enabling the identification of disease-causing variants, thus enhancing and confirming the diagnosis of mitochondrial disease in Puerto Ricans. We will be able to identify rare/novel variants specific to our Hispanic population, for both nuclear and mitochondrial DNA. DISCUSSION/SIGNIFICANCE OF FINDINGS: This study will help to characterize the metabolic profile of pediatric Puerto Ricans. No previous study has been reported that describes testing algorithms for genetic diagnosis of mitochondrial disease in our population. Variants found will contribute to a deep understanding of the genetic contribution to phenotypes and disease susceptibility.
Abstract
Human vertebral malformations (VMs) have an estimated incidence of 1/2000 and are associated with significant health problems including congenital scoliosis (CS) and recurrent organ system ...malformation syndromes such as VACTERL (vertebral anomalies; anal abnormalities; cardiac abnormalities; tracheo-esophageal fistula; renal anomalies; limb anomalies). The genetic cause for the vast majority of VMs are unknown. In a CS/VM patient cohort, three COL11A2 variants (R130W, R1407L and R1413H) were identified in two patients with cervical VM. A third patient with a T9 hemivertebra and the R130W variant was identified from a separate study. These substitutions are predicted to be damaging to protein function, and R130 and R1407 residues are conserved in zebrafish Col11a2. To determine the role for COL11A2 in vertebral development, CRISPR/Cas9 was used to create a nonsense mutation (col11a2L642*) as well as a full gene locus deletion (col11a2del) in zebrafish. Both col11a2L642*/L642* and col11a2del/del mutant zebrafish exhibit vertebral fusions in the caudal spine, which form due to mineralization across intervertebral segments. To determine the functional consequence of VM-associated variants, we assayed their ability to suppress col11a2del VM phenotypes following transgenic expression within the developing spine. While wildtype col11a2 expression suppresses fusions in col11a2del/+ and col11a2del/del backgrounds, patient missense variant-bearing col11a2 failed to rescue the loss-of-function phenotype in these animals. These results highlight an essential role for COL11A2 in vertebral development and support a pathogenic role for two missense variants in CS.
Spondylothoracic dysostosis (STD), also known as Jarcho-Levin syndrome (JLS), is a rare autosomal recessive disorder affecting the formation of the spine, characterized by a complete bilateral fusion ...of the ribs at the costovertebral junction, producing a "crablike" appearance of the thorax. Despite being declared a core indication for a V-osteotomy vertical expandable prosthetic titanium rib (VEPTR) expansion thoracoplasty of the posterior thorax, the natural history of STD in untreated subjects remains poorly documented. In this study, we report radiographic and pulmonary function findings and Patient-Reported Outcomes Measurement Information System (PROMIS) and 24-Item Early Onset Scoliosis Questionnaire (EOSQ-24) scores for untreated adult subjects with STD to gain insights into the natural history.
We identified 11 skeletally mature, untreated subjects with STD. Findings on medical evaluation, demographics, radiographic parameters, pulmonary function, genetic testing results, PROMIS measures, and EOSQ-24 scores were assessed.
Five male and 6 female subjects (mean age, 32.3 years range, 15 to 70 years) with a confirmed STD diagnosis based on radiographs and genetic testing were evaluated. Mean body mass index (BMI) was 24.4 kg/m 2 (range, 18 to 38.9 kg/m 2 ), and mean thoracic height was 16 cm (range, 12 to 17 cm). Pulmonary function tests (PFTs) showed a mean forced vital capacity (FVC) of 22% of predicted, mean forced expiratory volume in 1 second (FEV1) of 24% of predicted, and FEV1/FVC ratio of 107% of predicted. The mean PROMIS dyspnea score was 40 ± 8 points (range, 27.7 to 52.1 points). The mean total EOSQ-24 score was 77.3 ± 18 points (range, 43.9 to 93.2 points).
Our study characterizes the natural history of STD in untreated subjects. We confirmed the expected restrictive pattern in pulmonary function, but interestingly, our subjects exhibited better EOSQ scores compared with those reported in neuromuscular populations. PFT results and thoracic height did not correspond to PROMIS and EOSQ scores, questioning the use of those parameters as a surgical indication. We therefore suggest that the STD diagnosis as an absolute indication for VEPTR expansion thoracoplasty surgery be reconsidered.
Therapeutic Level IV . See Instructions for Authors for a complete description of levels of evidence.
OBJECTIVES/GOALS: Diagnostic odyssey is the time it can take to a patient for receiving a diagnosis. Diagnostic process in rare diseases can be complex due to the heterogeneity of symptoms and lack ...of access to care. We aim to evaluate the association between diagnostic odyssey, perceived stress, and access to care, in parents of Puerto Rican patients with a rare disease. METHODS/STUDY POPULATION: We propose a cross-sectional study in parents of 100 children who received an uninformative whole exome sequencing (WES) report during a scheduled appointment with their geneticist. Discussion of WES results during clinical session, followed by a Perceived Stress Scale (PSS-10) and semi-structured interview to explore the experience of access to care during the diagnostic process will be arranged. Observation and interviews will be recorded. Data analysis and descriptive statistics will be calculated using STATA. Statistical associations (OR) will be estimated using generalized linear models at a 5% significance level. RESULTS/ANTICIPATED RESULTS: We expect to find high perceived stress in parents of Puerto Rican pediatric individuals having rare diseases, especially among single mothers. We will be able to identify limited access to care in Puerto Rico, especially in the testing pre-authorization process and long waits for geneticist appointments. Demand for advanced diagnostics is above the number of medical geneticists available in Puerto Rico, which triggers delayed diagnosis, management, and counseling. Therefore, these could affect the health disparities in our population with rare diseases. DISCUSSION/SIGNIFICANCE: This descriptive study will evaluate perceived stress in parents of pediatric patients living a diagnostic odyssey in Puerto Rico. No study has described perceived stress and access to care in this Hispanic population with undiagnosed conditions. Findings will contribute to a deep understanding of diagnostic process and limited access to care.
Epigenetic mechanisms, genetic factors, and environment influence the diversity of phenotypes developed in various diseases. Duplications in several chromosomes are well characterized in the ...scientific literature, but partial duplications, in some cases, present with milder forms of a disease and are yet to be understood. Fortunately, the identification of genetic diseases has now become more feasible due to several cytogenetic techniques such as microarray analysis and karyotyping. With these tools, together with other laboratory results and clinical examination, we are able to report the first case in the medical literature of double partial trisomy of chromosome 9q34 and 16p13.
BACKGROUND Osteogenesis imperfecta is a skeletal disease with a range of phenotypes, depending on the genetic mutation. Individuals with osteogenesis imperfecta type I often have mutations in COL1A ...genes. This disease can be associated with chest wall deformities such as pectus excavatum, but the number of patients with this presentation is limited, and genetic variants associated with this phenotype have not been reported. CASE REPORT We studied the Skeletal Disorders Genetic Panel of 2 siblings with osteogenesis imperfecta type I and severe pectus excavatum requiring surgical correction. Both had severe respiratory symptoms secondary to the chest wall deformity, and the male patient had evidence of mitral valve insufficiency on an echocardiogram. Results of the genetic panel were remarkable for a homozygous copy number gain in exons 2 to 51 in gene COL1A1. Additionally, both had a heterozygous pathogenic variant in exon 7 of gene COL27A1 (replacement of a glycine with arginine in codon 697 of the protein). CONCLUSIONS Gene COL27A1 plays a role during the calcification of cartilage to bone and is associated with Steel syndrome, a skeletal disorder mainly found in the Puerto Rican population. Heterozygous carriers of the p.Gly697Arg variant in COL27A1 have not been described to have a phenotype with chest wall deformities. Additionally, a genotype-phenotype relationship regarding pectus excavatum in patients with osteogenesis imperfecta has not been described, suggesting that having COL1A gene mutations and simultaneous haploinsufficiency of COL27A1 can result in a phenotype of osteogenesis imperfecta with pectus excavatum and predispose these patients to additional phenotypic features.
PDF
