Single Pathogenic Variant Research Articles

Exon location of glycine substitutions impacts kidney survival in autosomal dominant Alport Syndrome.

Unlike X-linked or autosomal recessive Alport Syndrome, no clear genotype/phenotype correlation has yet been demonstrated in patients carrying a single variant of COL4A3 or COL4A4. We carried out a multicenter retrospective study to assess the risk factors involved in renal survival in patients presenting a single pathogenic variant on COL4A3 or COL4A4. 97 patients presenting a single pathogenic variant of COL4A3 or COL4A4 were included. The prevalence of end-stage kidney disease (ESKD) during follow-up was 28.7% (median age 47.5 years [IQR, 39.1-55.8]). 23 patients carried a 'severe' mutation (frameshift, stop gain, extensive deletion, impacting splicing), and 60 patients presented a glycine substitution in a collagenous domain. In patients with glycine missense variants, the location of the mutation in the distal exons was associated with worse renal survival with a more pronounced decline in eGFR compared to variants in proximal exons. Conversely, the presence of a severe mutation did not impact renal survival. Our results confirm that ADAS can lead to ESKD. We demonstrated that a glycine substitution involving the distal exons had a negative impact on renal survival in ADAS patients, probably due to a trimerization defect. This could help improve personalized follow-up in ADAS patients with glycine substitution and could be integrated to a future prognostic score to accurately predict renal outcomes.

Dominant negative ADA2 mutations cause ADA2 deficiency in heterozygous carriers.

Human ADA2 deficiency (DADA2) is an inborn error of immunity with a broad clinical phenotype which encompasses vasculopathy including livedo racemosa and lacunar strokes, as well as hemato-immunological features. Diagnosis is based on the combination of decreased serum ADA2 activity and the identification of biallelic deleterious alleles in the ADA2 gene. DADA2 carriers harbor a single pathogenic variant in ADA2 and are mostly considered healthy and asymptomatic. However, some DADA2 carriers present a phenotype compatible with DADA2. Here, we report ten patients from seven kindreds presenting with a phenotype indicative of DADA2, in whom only a single pathogenic variant (p.G47R, p.G47V, p.R169Q, p.H424N) was identified. To test whether being heterozygote for specific variants could explain the patients' phenotype, we investigated the effect of the ADA2 missense variants p.G47A, p.G47R, p.G47V, p.G47W, p.R169Q, p.E328K, p.T360A, p.N370K, p.H424N and p.Y453C on ADA2 protein expression, secretion and enzymatic activity. Functional studies indicate that they exert a dominant negative effect on ADA2 enzymatic activity, dimerization and/or secretion. At the molecular level, heterozygosity for these variants mimics what is observed in DADA2. We conclude that humans with heterozygous dominant negative missense variants in ADA2 are at risk of DADA2.

Characteristics of Chinese breast cancer patients with double heterozygosity for BRCA1 and BRCA2 germline pathogenic variants.

Despite of very rare, breast cancer patients with double heterozygosity (DH) variants in BRCA1 and BRCA2 genes have been identified in other ethnic groups and seem to be associated with distinctive phenotypes. However, little is known about the frequency and clinical characteristics of Chinese breast cancer patients with BRCA1/2 DH variants. Four hundred and eleven unrelated patients with BRCA1 or BRCA2 pathogenic variants (PVs) were identified in a large series of unselected breast cancer patients. Another two siblings with metachronous bilateral breast cancer were referred for genetic counseling, after which BRCA1/2 DH variants were detected. Four unrelated breast cancer patients with BRCA1/2 DH were identified in the cohort of 411 patients with BRCA1 or BRCA2 PVs, the frequency of BRCA1/2 DH was 0.97%. In total, six BRCA1/2 DH patients from five families were found in this study. In two families, the hereditary pattern of DH was speculated to have originated from both sides of the family. BRCA1/2 DH patients were more likely to have a family history of breast cancer than patients with a BRCA1 (100% vs. 29.2%, P = 0.004) or BRCA2 (100% vs. 29.6%, P = 0.004) single PV. BRCA1/2 DH patients were more likely to be triple-negative breast tumors than patients with single BRCA2 PVs (66.7% vs. 14.1%, P = 0.020), which was comparable to the findings in patients with single BRCA1 PVs (66.7% vs. 56.9%, P = 1.00). Chinese patients with BRCA1/2 DH exhibit a high percentage of family history of breast cancer. The tumor pathological features of BRCA1/2 DH carriers are similar to those of BRCA1 PV carriers.

Modeling Cortical Versus Hippocampal Network Dysfunction in a Human Brain Assembloid Model of Epilepsy and Intellectual Disability.

Neurodevelopmental disorders often impair multiple cognitive domains. For instance, a genetic epilepsy syndrome might cause seizures due to cortical hyperexcitability and present with memory impairments arising from hippocampal dysfunction. This study examines how a single disorder differentially affects distinct brain regions by using human patient iPSC-derived cortical- and hippocampal-ganglionic eminence assembloids to model Developmental and Epileptic Encephalopathy 13 (DEE-13), a condition arising from gain-of-function mutations in the SCN8A gene. While cortical assembloids showed network hyperexcitability akin to epileptogenic tissue, hippocampal assembloids did not, and instead displayed network dysregulation patterns similar to in vivo hippocampal recordings from epilepsy patients. Predictive computational modeling, immunohistochemistry, and single-nucleus RNA sequencing revealed changes in excitatory and inhibitory neuron organization that were specific to hippocampal assembloids. These findings highlight the unique impacts of a single pathogenic variant across brain regions and establish hippocampal assembloids as a platform for studying neurodevelopmental disorders.

Population Screening for Hereditary Haemochromatosis-Should It Be Carried Out, and If So, How?

The Human Genome Project, completed in 2003, heralded a new era in precision medicine. Somewhat tempering the excitement of the elucidation of the human genome is the emerging recognition that there are fewer single gene disorders than first anticipated, with most diseases predicted to be polygenic or at least gene-environment modified. Hereditary haemochromatosis (HH) is an inherited iron overload disorder, for which the vast majority of affected individuals (>90%) have homozygosity for a single pathogenic variant in the HFE gene, resulting in p.Cys282Tyr. Further, there is significant benefit to an individual in identifying the genetic risk of HH, since the condition evolves over decades, and the opportunity to intervene and prevent disease is both simple and highly effective through regular venesection. Add to that the immediate benefit to society of an increased pool of ready blood donors (blood obtained from HH venesections can generally be used for donation), and the case for population screening to identify those genetically at risk for HH becomes more cogent. Concerns about genetic discrimination, creating a cohort of "worried well", antipathy to acting on medical advice to undertake preventive venesection or simply not understanding the genetic risk of the condition adequately have all been allayed by a number of investigations. So why then has HH population genetic screening not been routinely implemented anywhere in the world? The answer is complex, but in this article we explore the pros and cons of screening for HH and the different views regarding whether it should be phenotypic (screening for iron overload by serum ferritin and/or transferrin saturation) or genotypic (testing for HFE p.Cys282Tyr). We argue that now is the time to give this poster child for population genetic screening the due consideration required to benefit the millions of individuals at risk of HFE-related iron overload.

CVID With Unusual Peripheral Mononeuropathy and Associated IL-7 Receptor Mutation.

Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency. It is characterized by hypogammaglobulinemia and can present with a broad range of symptoms including recurrent bacterial infections, autoimmunity, and malignancy. Rarely, it has been implicated with peripheral neuropathy. We present a case of CVID with peripheral neuropathy and a pathogenic heterozygous variant of IL-7 receptor gene. The patient is a 38-year-old female with a history of recurrent infections since childhood including pneumonia and sinus infections status post tonsillectomy and sinus surgery. She subsequently developed severe left leg and lower back pain that progressed to left foot drop and decreased sensation over the left leg. She was found to have severe hypogammaglobulinemia and poor polysaccharide and protein response, thus meeting criteria for CVID. Mononeuropathy is a rare finding in CVID. Genetic panel was performed and was significant for a single pathogenic variant in IL-7 receptor. Disruptions in the IL-7 and IL-7 receptor signaling pathway have been associated with autoimmunity such as rheumatoid arthritis and multiple sclerosis. Further investigation is indicated to determine the clinical significance of this variant.

Infant glycogen storage disease type Ⅳ: a clinicopathological and genetic characteristics analysis of five cases

Objective: To investigate the clinical pathology and gene mutation characteristics of patients with glycogen storage disease type Ⅳ (GSD Ⅳ). Methods: The clinical data, liver histopathology and ultrastructural morphology, and gene sequencing results of 5 GSD Ⅳ cases diagnosed in the Children's Hospital Affiliated to Shanghai Jiaotong University School of Medicine and the Children's Hospital of Fudan University from January 2015 to February 2022 were collected and analyzed retrospectively. Results: Among the 5 cases, 3 were male and 2 were female, ranging in age from 4 months to 1 year and 9 months. The clinical manifestations included fever, hepatosplenomegaly, liver insufficiency, growth retardation and hypotonia. Four cases had liver biopsy showing ground-glass-like changes in hepatocytes with intracytoplasmic inclusion bodies and varying degrees of fibrosis. Liver electron microscopy in 2 cases showed that the level of glycogen increased to varying degrees, and the cytoplasm was filled with low electron density substances. Genetic testing revealed that 3 cases had compound heterozygous variants in GBE1 gene; 1 case had a single pathogenic variant in GBE1 gene; and 1 case was deceased with no genetic testing, but each parent was tested for a heterozygous variant in the GBE1 gene. A total of 9 GBE1 gene mutations were detected, 3 of which were reported mutations and 6 novel mutations. One case died of liver cirrhosis, and 1 case underwent autologous liver transplantation. After transplantation, the liver function basically returned to normal, and the growth and development improved; the other 3 cases were managed through diet control and symptomatic treatment. Conclusions: CSD Ⅳ is an extremely rare inherited metabolic disease caused by GBE1 gene mutation, often presenting with hepatic and neuromuscular disorders, with heterogeneous clinical manifestations. The diagnosis mainly depends on histopathology and a pedigree gene analysis.

Most Fanconi anemia heterozygotes are not at increased cancer risk: A genome-first DiscovEHR cohort population study

PurposeFanconi anemia (FA) is a bone marrow failure and cancer predisposition syndrome caused primarily by biallelic pathogenic variants in 1 of 22 genes involved in DNA interstrand cross-link repair. An enduring question concerns cancer risk of those with a single pathogenic FA gene variant. To investigate all FA genes, this study utilized the DiscovEHR cohort of 170,503 individuals with exome sequencing and electronic health data. Methods5822 subjects with a single pathogenic variant in an FA gene were identified. Two control groups were used in primary analysis deriving cancer risk signals. Secondary exploratory analysis was conducted using the UK Biobank and The Cancer Genome Atlas. ResultsSignals for elevated cancer risk were found in all 5 known cancer predisposition genes. Among the remaining 15 genes associated with autosomal recessive inheritance cancer risk signals were found for 4 cancers across 3 genes in the primary cohort but were not validated in secondary cohorts. ConclusionTo our knowledge, this is the first and largest FA heterozygote study to use genomic ascertainment and validates well-established cancer predispositions in 5 genes, whereas finding insufficient evidence of predisposition in 15 others. Our findings inform clinical surveillance given how common pathogenic FA variants are in the population.

Spastic Paraplegia Type 7-Associated Optic Neuropathy: A Case Series.

Hereditary optic neuropathies comprise a group of clinically and genetically heterogeneous disorders. Optic neuropathy has been previously reported in families with spastic paraplegia type 7 (SPG7) gene mutations. However, the typical time course and clinical presentation of SPG7-associated optic neuropathy is poorly understood. We report a series of 5 patients harboring pathogenic SPG7 mutations who originally presented to a neuro-ophthalmology clinic with symptoms of optic neuropathy. Retrospective case series of 5 patients with pathogenic SPG7 mutations and optic atrophy from 3 neuro-ophthalmology clinics. Demographic, clinical, diagnostic, and treatment data were collected and reported by the clinician authors. Five patients ranging in age from 8 to 48 years were evaluated in the neuro-ophthalmology clinic. Although there were variable clinical presentations for each subject, all noted progressive vision loss, typically bilateral, and several also had previous diagnoses of peripheral neuropathy (e.g., Guillain-Barré Syndrome). Patients underwent neuro-ophthalmic examinations and testing with visual fields and optic coherence tomography of the retinal nerve fiber layer. Genetic testing revealed pathogenic variants in the SPG7 gene. Five patients presented to the neuro-ophthalmology clinic with progressive vision loss and were diagnosed with optic atrophy. Although each patient harbored an SPG7 mutation, this cohort was phenotypically and genotypically heterogeneous. Three patients carried the Ala510Val variant. The patients demonstrated varying degrees of visual acuity and visual field loss, although evaluations were completed during different stages of disease progression. Four patients had a previous diagnosis of peripheral neuropathy. This raises the prospect that a single pathogenic variant of SPG7 may be associated with peripheral neuropathy in addition to optic neuropathy. These results support the consideration of SPG7 testing in patients with high suspicion for genetic optic neuropathy, as manifested by symmetric papillomacular bundle damage without clear etiology on initial workup. Applied judiciously, genetic testing, including for SPG7, may help clarify the cause of unexplained progressive optic neuropathies.

Genetic Identification of Homozygous Familial Hypercholesterolemia by Long-Read Sequencing Among Patients With Clinically Diagnosed Heterozygous Familial Hypercholesterolemia.

Homozygous familial hypercholesterolemia (HoFH) is a rare genetic disorder characterized by extremely elevated plasma LDL-C (low-density lipoprotein cholesterol) and accelerated atherosclerosis. Accurate identification of patients with HoFH is essential as they may be eligible for specialized treatments. We hypothesized that a subset of patients with clinically diagnosed heterozygous FH (HeFH) may in fact have HoFH, and this could be identified by genetic diagnosis. We recruited patients with a clinical diagnosis of HeFH based on a Dutch Lipid Clinic Network score ≥6 and no secondary cause of hypercholesterolemia. We performed targeted next-generation sequencing of the LDLR, APOB, PCSK9, and LDLRAP1 genes, followed by long-read sequencing of the LDLR gene in patients with >1 pathogenic LDLR variant. We examined lipid levels and cardiovascular events. Among 705 patients with clinically diagnosed HeFH, we identified a single pathogenic variant in 300 (42.6%) and >1 pathogenic variant in the LDLR gene in 11 patients (1.6%). We established a genetic diagnosis of HoFH in 6 (0.9%) patients (3 true homozygotes and 3 compound heterozygotes). The mean baseline LDL-C and prevalence of premature cardiovascular disease of patients with genetically identified HoFH was significantly higher than patients with HeFH. In a cohort of patients with clinically diagnosed HeFH, genetic testing including long-read sequencing revealed that 0.9% had HoFH. These patients tended to have a more severe clinical phenotype. Genetic testing of patients with clinical FH may identify patients with HoFH that had eluded clinical diagnosis.

Germline variants associated with breast cancer in Khakass women of North Asia.

Variants in the BRCA1/2 genes are responsible for familial breast cancer. Numerous studies showed a different spectrum of BRCA variants among breast cancer patients of different Ethnicity origin. In the available literature, no previous research has focused on breast cancer-associated variants among the Khakass people (the indigenous people of the Russian Federation). Twenty-six Khakass breast cancer patients were enrolled in the study. Genomic DNA was isolated from blood samples and used to prepare libraries using a Hereditary Cancer Solution kit. Next-generation sequencing (NGS) was performed using the MiSeq System (Illumina, USA). In our study, 12% of patients (3/26) carried a single pathogenic variant; 54% of patients (14/26) carried variants of uncertain significance (VUS) or conflicting variants; and 35% of patients (9/26) did not carry any clinically significant variants. Germline pathogenic variant in the ATM gene (rs780619951, NC_000011.10:g.108259022C > T) was identified in two unrelated patients with a family history of cancer (7.6%, 2/26). The pathogenic truncating variant in the ATM gene (p. R805* or c.2413C > T) leads to the nonfunctional version of the protein. This variant has been earlier reported in individuals with a family history of breast cancer. Our pilot study describes the germline variant in the ATM gene associated with breast cancer in Khakass women of North Asia.

Gain- and Loss-of-Function CFTR Alleles Are Associated with COVID-19 Clinical Outcomes.

Carriers of single pathogenic variants of the CFTR (cystic fibrosis transmembrane conductance regulator) gene have a higher risk of severe COVID-19 and 14-day death. The machine learning post-Mendelian model pinpointed CFTR as a bidirectional modulator of COVID-19 outcomes. Here, we demonstrate that the rare complex allele [G576V;R668C] is associated with a milder disease via a gain-of-function mechanism. Conversely, CFTR ultra-rare alleles with reduced function are associated with disease severity either alone (dominant disorder) or with another hypomorphic allele in the second chromosome (recessive disorder) with a global residual CFTR activity between 50 to 91%. Furthermore, we characterized novel CFTR complex alleles, including [A238V;F508del], [R74W;D1270N;V201M], [I1027T;F508del], [I506V;D1168G], and simple alleles, including R347C, F1052V, Y625N, I328V, K68E, A309D, A252T, G542*, V562I, R1066H, I506V, I807M, which lead to a reduced CFTR function and thus, to more severe COVID-19. In conclusion, CFTR genetic analysis is an important tool in identifying patients at risk of severe COVID-19.

Abstract 13821: Genetic Identification of Homozygous Familial Hypercholesterolemia by Long-Read Sequencing Among Patients With Clinically Diagnosed Heterozygous Familial Hypercholesterolemia

Background: Homozygous Familial Hypercholesterolemia (HoFH) is a rare genetic disorder characterized by extremely elevated plasma low-density lipoprotein cholesterol (LDL-C) and accelerated atherosclerosis. Accurate identification of patients with HoFH is essential as they may be eligible for specialized treatments. The objective of this study was to identify and characterize patients with HoFH among patients with clinically diagnosed heterozygous FH (HeFH). Methods: We studied patients from the British Columbia FH Registry with a Dutch Lipid Clinic Network score ≥6 and no secondary cause of hypercholesterolemia. We performed targeted next-generation sequencing of the LDLR , APOB , PCSK9 and LDLRAP1 genes. Long-read sequencing of the LDLR gene was subsequently done for patients with >1 pathogenic LDLR variant to determine haplotypes. We examined lipid levels and cardiovascular events (unstable angina, myocardial infarction and coronary revascularization). Results: Among 705 patients with clinically diagnosed HeFH, we identified a single pathogenic variant in 300 (42.6%) patients and >1 pathogenic variant in the LDLR gene in 11 (1.6%) patients. We established a genetic diagnosis of HoFH in 6 (0.9%) patients (3 true homozygous and 3 compound heterozygous in trans). The mean baseline LDL-C of genetically identified HoFH patients was significantly higher than those with 1 variant. The prevalence of premature cardiovascular disease was numerically greater in the genetically identified HoFH group (29.4% vs 18.0%, p=0.2). Conclusions: In a cohort of patients with clinically diagnosed HeFH, genetic testing by long-read sequencing revealed that 0.9% had HoFH. These patients tended to have a more severe phenotype. Genetic testing of patients with clinical FH may identify patients with HoFH that had eluded clinical diagnosis.

LATE-ONSET COMBINED IMMUNE DEFICIENCY IN A PATIENT WITH ADENOSINE DEAMINASE GENE MUTATION

<h3>Introduction</h3> We report on a 25-year-old man with a history of recurrent pneumonia and large joint infections who was found to have T cell dysfunction with B cell lymphopenia and a heterozygous adenosine deaminase(ADA) gene mutation. <h3>Case Description</h3> The patient has had three large joint infections and three-to-four episodes of pneumonia in his life. He is without other prior medical condition or family history of immune deficiency. He presented to the ER with tachycardia and left knee swelling. He was found to have pseudomonas bacteremia of unknown source for which he was treated. Due to his tachycardia, he had a chest CT to evaluate for pulmonary embolism which revealed found incidental bronchiectasis. Evaluation for immune deficiency was initiated and he was found to have IgA <10 mg/dL, IgG <75, and IgM <20, CD4 count 202 cells/uL, CD8 596, low response to polysaccharide and protein vaccines. HIV testing was negative. We then pursued genetic testing. Patient was found to carry a single pathogenic variant in the ADA gene. Loss of function variants in this gene are associated with severe combined immunodeficiency, but a second variant was not identified. Our patient is doing well on IVIG without further infections. <h3>Discussion</h3> To our knowledge, our patient is the first reported to be a carrier for a pathogenic ADA gene mutation and presenting with a clinical phenotype of B cell lymphopenia and T cell dysfunction. A more complete understanding of the underlying genetic causes for late-onset combined immune deficiency is needed as well as any correlation with ADA deficiency.

COMMON VARIABLE IMMUNODEFICIENCY WITH UNUSUAL PERIPHERAL NEUROPATHY AND ASSOCIATED IL-7 RECEPTOR MUTATION

<h3>Introduction</h3> Common variable immunodeficiency is the most common symptomatic primary immunodeficiency, characterized by hypogammaglobulinemia and presenting with a broad range of symptoms including recurrent bacterial infections, autoimmunity, and neoplastic conditions. We present a case of common variable immunodeficiency associated with peripheral neuropathy and a pathogenic heterozygous variant of interleukin-7 receptor (IL7R) gene. <h3>Case Description</h3> The patient is a thirty-eight-year-old female with a history of recurrent infections since childhood including pneumonia and sinus infections status post-tonsillectomy and sinus surgery. She subsequently developed severe left leg and lower back pain which progressed to left foot drop and decreased sensation over the leg with accompanied paresthesia. Labs showed profound hypogammaglobulinemia with scarce levels of IgG (55mg/dl) and IgM (21mg/dl) and lack of IgA (2mg/dl) and IgE (<0.3 IU/ml). Further workup included normal lymphocyte proliferation with deficient polysaccharide and protein response. The patient's lack of IgG antibody production is an important criterion for the diagnosis of common variable immunodeficiency. Genetic panel was performed and significant for a single pathogenic variant in IL7R. <h3>Discussion</h3> We present a case of recurrent sinopulmonary infections with associated peripheral neuropathy prompting further evaluation, revealing the diagnosis of common variable immunodeficiency. Mononeuropathy is a rare finding in common variable immunodeficiency, although should elicit further evaluation if the etiology is unclear. Additional workup was significant for a single pathogenic variant in IL7R. This gene is associated with autosomal recessive severe combined immunodeficiency when homozygous. Further genetic testing is indicated to determine the clinical significance of this variant.

Increased Co-Occurrence of Pathogenic Variants in Hereditary Breast and Ovarian Cancer and Lynch Syndromes: A Consequence of Multigene Panel Genetic Testing?

The probability of carrying two pathogenic variants (PVs) in dominant cancer-predisposing genes for hereditary breast and ovarian cancer and lynch syndromes in the same patient is uncommon, except in populations where founder effects exist. Two breast cancer women that are double heterozygotes (DH) for both BRCA1/BRCA2, one ovarian cancer case DH for BRCA1/RAD51C, and another breast and colorectal cancer who is DH for BRCA2/PMS2 were identified in our cohort. Ages at diagnosis and severity of disease in BRCA1/BRCA2 DH resembled BRCA1 single-carrier features. Similarly, the co-existence of the BRCA2 and PMS2 mutations prompted the development of breast and colorectal cancer in the same patient. The first BRCA1/BRCA2 DH was identified by HA-based and Sanger sequencing (1 of 623 families with BRCA PVs). However, this ratio has increased up to 2.9% (1 DH carrier vs. 103 single PV carriers) since using a custom 35-cancer gene on-demand panel. The type of cancer developed in each DH patient was consistent with the independently inherited condition, and the clinical outcome was no worse than in patients with single BRCA1 mutations. Therefore, the clinical impact, especially in patients with two hereditary syndromes, lies in genetic counseling tailor-made for each family based on the clinical guidelines for each syndrome. The number of DH is expected to be increased in the future as a result of next generation sequencing routines.

Differences in Motor Features of C9orf72, MAPT, or GRN Variant Carriers With Familial Frontotemporal Lobar Degeneration.

Familial frontotemporal lobar degeneration (f-FTLD) is a phenotypically heterogeneous spectrum of neurodegenerative disorders most often caused by variants within chromosome 9 open reading frame 72 (C9orf72), microtubule-associated protein tau (MAPT), or granulin (GRN). The phenotypic association with each of these genes is incompletely understood. We hypothesized that the frequency of specific clinical features would correspond with different genes. We screened the Advancing Research and Treatment in Frontotemporal Lobar Degeneration (ARTFL)/Longitudinal Evaluation of Familial Frontotemporal Dementia Subjects (LEFFTDS)/ARTFL LEFFTDS Longitudinal Frontotemporal Lobar Degeneration Consortium for symptomatic carriers of pathogenic variants in C9orf72, MAPT, or GRN. We assessed for clinical differences among these 3 groups based on data recorded as part of a detailed neurologic examination, the Progressive Supranuclear Palsy Rating Scale, Progressive Supranuclear Palsy-Quality of Life Rating Scale, Unified Parkinson's Disease Rating Scale Part III (motor items), and the Amyotrophic Lateral Sclerosis Functional Rating Scale, revised version. Data were analyzed using Kruskal-Wallis and Wilcoxon rank-sum tests and Fisher exact test. We identified 184 symptomatic participants who had a single pathogenic variant in C9orf72 (n = 88), MAPT (n = 53), or GRN (n = 43). Motor symptom age at onset was earliest in the MAPT participants followed by C9orf72, whereas the GRN pathogenic variant carriers developed symptoms later. C9orf72 participants more often had fasciculations, muscle atrophy, and weakness, whereas parkinsonism was less frequent. Vertical oculomotor abnormalities were more common in the MAPT cohort, whereas apraxia and focal limb dystonia occurred more often in participants with GRN variants. We present a large comparative study of motor features in C9orf72, MAPT, and GRN pathogenic variant carriers with symptomatic f-FTLD. Our findings demonstrate characteristic phenotypic differences corresponding with specific gene variants that increase our understanding of the genotype-phenotype relationship in this complex spectrum of neurodegenerative disorders. NCT02365922, NCT02372773, and NCT04363684.

Unveiling Compound Heterozygous Familial Hypercholesterolemia

Lead Author's Financial Disclosures Nothing to disclose. Study Funding None. Background/Synopsis A 38-year-old female with a history of hypercholesterolemia as well as a family history of hypercholesterolemia in mother diagnosed at age 68 and in young daughter at age 11 is referred for further evaluation and management of hypercholesterolemia. Objective/Purpose To review the role of genetic testing in management of severe hypercholesterolemia. Methods In addition to routine clinical care, genetic testing was completed by Invitae using gene sequencing and deletion/duplication analysis with next generation sequencing technology (NGS). Results A 38-year-old female has been treated since age 20, when she was first found to have high cholesterol. She is referred for further evaluation after her 11-year-old daughter is noted to have high cholesterol. Invitae Familial Hypercholesterolemia Panel identified a LDLR: c.1027 G>A (p.Gly343Ser) pathogenic variant and LDLR: c.1880 C>T (p.Ala627Val) variant of uncertain significance (VUS). Conclusions Familial hypercholesterolemia (FH) is the most common inherited cardiovascular disease, with a prevalence of 1 in 311, characterized by significantly elevated LDL cholesterol (LDL-C) and responsible for up to 2%-3% of heart attacks in individuals younger than age 60 years. In fact, men with FH who are untreated have a 50% chance of having a coronary event by age 50 and untreated women have a 30% risk by age 60. FH is caused by pathogenic (disease-causing) variants in four major genes: APOB, LDLR, LDLRAP1, PCSK9. The severity of the LDL-C elevation can be determined by the specific variant's impact on LDL-receptor activity and function, and/or the impact from other genes that raise and/or lower the LDL-C. Pathogenic variants in the APOB and PCSK9 and additional LDLR variants may be present as well and are described as double heterozygotes if different genes are affected, compound heterozygotes if different alleles in the same gene are affected, or homozygous if 2 copies of the pathogenic variant is found. In our clinical case, genetic testing revealed a pathogenic variant in the LDLR gene, c.1027 G>A (p.Gly343Ser). This gene is responsible for effective transport of LDL cholesterol into the cell, when defective leads to build up of the un-transported cholesterol in blood vessels. In addition to the pathogenic LDLR variant, a VUS in the LDLR gene, c.1880 C>T (p.Ala627Val) was identified. Variants are of uncertain significance generally do not have evidence to determine pathogenicity with little to no direct impact on phenotype. For now, our patient should be considered heterozygous FH based upon the single pathogenic variant. However, given the supporting evidence and expectation that the VUS is likely pathogenic, we did advise her that the genetic description may change to compound heterozygous depending upon database expansion. Of note, the underrepresentation of this variant in existing databases may reflect sampling bias. Our patient is of Afro-Caribbean (Haitian) heritage, which is a population that has been underrepresented in medical studies. Nothing to disclose.

Geographical distribution of cystic fibrosis carriers as population genetic determinant of COVID-19 spread and fatality in 37 countries

COVID-19 has shown a relevant heterogeneity in spread and fatality among countries together with a significant variability in its clinical presentation, indicating that host genetic factors may influence COVID-19 pathogenicity. Indeed, subjects carrying single pathogenic variants of the Cystic Fibrosis (CF) Transmembrane Conductance Regulator (CFTR) gene – i.e. CF carriers – are more susceptible to respiratory tract infections and are more likely to undergo severe COVID-19 with higher risk of 14-day mortality.Given that CF carrier prevalence varies among ethnicities and nations, an ecological study in 37 countries was conducted, in order to determine to what extent the diverse CF carrier geographical distribution may have affected COVID-19 spread and fatality during the first pandemic wave.The CF prevalence in countries, as indicator of the geographical distribution of CF carriers, significantly correlated in a direct manner with both COVID-19 prevalence and its Case Fatality Rate (CFR). In a regression study weighted for the number of tests performed, COVID-19 prevalence positively correlated with CF prevalence, while CFR correlated with population percentage older than 65-year, cancer and CF prevalence. Multivariate regression model also confirmed COVID-19 CFR to be associated with CF prevalence, after adjusting for elderly, cancer prevalence, and weighting for the number of tests performed.This study suggests a putative contribution of population genetics of CFTR in understanding the spatial distribution of COVID-19 spread and fatality.

32. Genetic testing for individuals with non-syndromic differences in sex development (DSD): collaborative approach yields results

Differences of Sex Development (DSD) are a group of conditions in which there is atypical anatomic, gonadal, or chromosomal sex. With input from multiple stakeholders, our laboratory recently validated a genetic testing panel for non-syndromic DSD, which utilizes targeted next generation sequencing and exon-level microarray analysis. Data from the first 37 consecutive tests is presented here. The majority of patients in this cohort were evaluated in our institution's DSD clinic, which includes providers specializing in pediatric and reproductive endocrinology, genetics, urology, gynecology and child and adolescent psychology. Almost all patients had prior karyotype, SRY FISH, and/or chromosomal microarray testing. Exclusion criteria for panel testing included the presence of syndromic features or suspected 21-hydryoxylase deficiency. Pathogenic or likely pathogenic variants in genes associated with dominant conditions were reported for 15 (40.5%) individuals. The pathogenic and likely pathogenic variants were identified in 10 different genes: AMH, AMHR2, ANOS1, AR (in 5 unrelated individuals), CYP17A1, MAMLD1 (in two unrelated individuals), MAP3K1, PROKR2, SRY, and STAR. For 3 other individuals (8%), a single pathogenic variant was reported in a gene associated with a recessive condition. Variants of uncertain clinical significance were reported for 5 individuals (13.5%), and no variants were reported for 14 individuals (38%). Close collaboration between the laboratory and the clinical team during the test validation process, as well as ongoing discussions surrounding test utilization, enabled development of a panel most appropriate for our patient population, with a high diagnostic rate. The targeted panel approach avoided issues related to incidental findings and contributed to the lower rate of reported variants of uncertain significance. Future goals for the DSD panel include streamlining the laboratory workflow and regular updates to panel content to include genes recently implicated in DSD-related conditions.