Homozygous Deleterious Variant Research Articles

Subacute Partially Reversible Leukoencephalopathy Expands the Aicardi-Goutières Syndrome Phenotype.

To report a series of atypical presentations of Aicardi-Goutières syndrome. Clinical, neuroimaging, and genetic data. We report a series of six unrelated patients (five males) with a subacute loss of developmental milestones, pyramidal signs, and regression of communication abilities, with onset at ages ranging from 7 to 20 months, reaching a nadir after 4 to 24 weeks. A remarkable improvement of lost abilities occurred in the follow-up, and they remained with residual spasticity and dysarthria but preserved cognitive function. Immunization or febrile illness occurred before disease onset in all patients. CSF was normal in two patients, and in four, borderline or mild lymphocytosis was present. A brain CT scan disclosed a subtle basal ganglia calcification in one of six patients. Brain MRI showed asymmetric signal abnormalities of white matter with centrum semi-ovale involvement in five patients and a diffuse white matter abnormality with contrast enhancement in one. Four patients were diagnosed and treated for acute demyelinating encephalomyelitis (ADEM). Brain imaging was markedly improved with one year or more of follow-up (average of 7 years), but patients remained with residual spasticity and dysarthria without cognitive impairment. Demyelination relapse occurred in a single patient four years after the first event. Whole-exome sequencing (WES) was performed in all patients: four of them disclosed biallelic pathogenic variants in RNASEH2B (three homozygous p.Ala177Thr and one compound heterozygous p.Ala177Thr/p.Gln58*) and in two of them the same homozygous deleterious variants in RNASEH2A (p.Ala249Val). This report expands the phenotype of AGS to include subacute developmental regression with partial clinical and neuroimaging improvement. Those clinical features might be misdiagnosed as ADEM.

Biallelic deleterious germline SH2B3 variants cause a novel syndrome of myeloproliferation and multi-organ autoimmunity.

SH2B3 is a negative regulator of multiple cytokine receptor signalling pathways in haematopoietic tissue. To date, a single kindred has been described with germline biallelic loss-of-function SH2B3 variants characterized by early onset developmental delay, hepatosplenomegaly and autoimmune thyroiditis/hepatitis. Herein, we described two further unrelated kindreds with germline biallelic loss-of-function SH2B3 variants that show striking phenotypic similarity to each other as well as to the previous kindred of myeloproliferation and multi-organ autoimmunity. One proband also suffered severe thrombotic complications. CRISPR-Cas9 gene editing of zebrafish sh2b3 created assorted deleterious variants in F0 crispants, which manifest significantly increased number of macrophages and thrombocytes, partially replicating the human phenotype. Treatment of the sh2b3 crispant fish with ruxolitinib intercepted this myeloproliferative phenotype. Skin-derived fibroblasts from one patient demonstrated increased phosphorylation of JAK2 and STAT5 after stimulation with IL-3, GH, GM-CSF and EPO compared to healthy controls. In conclusion, these additional probands and functional data in combination with the previous kindred provide sufficient evidence for biallelic homozygous deleterious variants in SH2B3 to be considered a valid gene-disease association for a clinical syndrome of bone marrow myeloproliferation and multi-organ autoimmune manifestations.

Biallelic Deleterious Germline SH2B3 Variants Cause a Novel Clinical Syndrome of Myeloproliferation and Multi-Organ Autoimmunity

SH2B3 is a negative regulator of cytokine receptor signalling pathways in hematopoietic tissue. Acquired deleterious SH2B3 variants resulting in increased JAK/STAT signalling are observed in myeloproliferative neoplasms (MPN) however the clinical implications and phenotype of deleterious germline variants in SH2B3 are less clear. A single consanguineous kindred has been previously described with homozygous deleterious germline SH2B3 variants presenting with hepatosplenomegaly, autoimmune hepatitis, developmental delay, autoimmune thyroiditis and acute lymphoblastic leukemia (Perez-Garcia, A., et al, Blood, 2013), however a clinically valid gene-disease pair according to formal criteria has not been met to date for SH2B3. We identified two probands from unrelated kindred with germline homozygous deleterious SH2B3 variants. The first patient presented with splenomegaly, thrombocytosis, neutrophilia and a leukoerythroblastic blood film at 3 months old. He developed alopecia areata at 2 years and autoimmune hypothyroidism at 6 years. He was otherwise developmentally normal without any detected liver abnormalities or thrombotic episodes. Whilst his splenomegaly and neutrophil count gradually improved throughout life, his platelet count remained markedly elevated (~1000x109/L at 18 years of age). Targeted NGS identified a homozygous frameshift variant in SH2B3 (NM_005475.3:c.441_468del; p.(Arg148Profs*40)). Both parents were heterozygous carriers of this variant. The second patient was a male born to consanguineous parents and noted shortly after birth to have isolated splenomegaly. He was diagnosed with autoimmune hypothyroidism and Raynaud syndrome at 12 years and was noted to have a persistent thrombocytosis ranging from 550 - 780 x109/L. He developed autoimmune hepatitis and insulin dependent diabetes at 17 years and around the same time he also suffered a right-sided middle cerebral artery territory infarct with a right carotid artery thrombus. Whole genome sequencing detected a homozygous missense variant in SH2B3 (NM_005475.3:c.1204G>A; p.(Val402Met)) in the patient with both parents being heterozygous carriers. In order to understand these variants further we modelled the human p.(Arg148Profs*40) variant from patient 1 in zebrafish. CRISPR-Cas9 gene editing was targeted to the analogous region of zebrafish sh2b3 to create assorted carboxyl-truncating mutations in F0 crispants. On-target gene-editing was verified by Sanger sequencing and NGS. F0 crispants had a significantly increased number of macrophages and CD41-expressing cells (HSCs and thrombocytes), replicating the patient phenotype. Treatment of the sh2b3 crispant fish with the JAK inhibitor ruxolitinib intercepted the myeloproliferative phenotype. The myeloproliferative phenotype was not observed in stable deletion mutants, likely reflecting genetic compensation not present in crispants. Skin-derived fibroblasts from patient 2 who carried the Val402Met homozygous variant, showed increased phosphorylation of JAK2, STAT5 and STAT3 by immunoblotting after stimulation with IL3, GH, GM-CSF and EPO compared to healthy controls. In conclusion, these newly described kindreds showing striking phenotypic similarity to each other as well as the previously described kindred and in conjunction with our functional data provide sufficient evidence for biallelic homozygous deleterious variants in SH2B3 to be considered a valid gene-disease association with a clinical syndrome of bone marrow myeloproliferation and multi-organ autoimmune manifestations. Notably, neither of our patients had evidence of acute lymphoblastic leukemia or overt hematological malignancy and further affected individuals will need to be described in order to fully understand the breadth of the phenotype. Moreover, our data supports ruxolitinib as being a potential therapeutic option for patients with this rare novel immune dysregulatory syndrome.

Homozygous variants in AKAP3 induce asthenoteratozoospermia and male infertility

BackgroundAs a common type of asthenoteratozoospermia, multiple morphological abnormalities of the sperm flagella (MMAF) can cause male infertility. Previous studies have revealed genetic factors as a major cause of MMAF....

A Novel Variant of Adenosine Deaminase 2 Deficiency Presented With Chronic Thrombocytopenia, Anemia, and Early-Onset Stroke

Deficiency of adenosine deaminase 2 (DADA2) is a rare recessive disorder caused by the bi-allelic loss-of-function pathogenic variants in the ADA2 gene (MIM: 607575, also known as CECR1, cat eye syndrome chromosome region, candidate 1). Based on the Human Gene Mutation Database (HGMD®), 53 different disease-causing variants have been identified in this gene to date. This case report aims to describe a new vasculitis, autoinflammation, immunodeficiency, and hematologic defects syndrome (VAIHS) case caused by a novel pathogenic variant. A four-year-old boy was referred to our hospital with anemia, thrombocytopenia, and stroke, but no skin manifestations. The patient had a significant phenotypic overlap with VAIHS. Molecular genetic analysis via whole exome sequencing identified a homozygous deleterious variant in ADA2. To our knowledge, the identified variant has never been described in the literature. Screening for ADA2 pathogenic variants should be considered in the differential diagnosis of pediatric patients manifesting with chronic thrombocytopenia or early-onset stroke for an accurate diagnosis and appropriate treatment choices.

CRADD and USP44 mutations in intellectual disability, mild lissencephaly, brain atrophy, developmental delay, strabismus, behavioural problems and skeletal anomalies

In a consanguineous Pakistani kinship afflicted with mild to moderate intellectual disability (ID), mild lissencephaly, brain atrophy and skeletal anomalies, we detected homozygous CRADD c.2T > G (p.Met1?) and USP44 c.873_886delinsT (p.Leu291Phefs*8), two good candidates 1.85-Mb apart that segregated with the disorder. Biallelic damaging variants in CRADD cause recessive mental retardation-34 (MRT34; MIM 614499) with mild to moderate ID, “thin” lissencephaly, and variable megalencephaly and seizures. For USP44, only a single ID family has been reported with a homozygous deleterious variant, which is the same as the variant we detected. In affected individuals we present, at ages 29–32 years, clinical findings are similar yet not fully concordant with phenotypes for either gene considering the skeletal findings, and ID is not as severe as would be expected for defects in two genes with additive effect. Some variable CRADD-related features such as language impairment and seizures are not observed in the presented family. The presence of the two variants in the family is a very rare example of familial linked homozygous variants, and whether the damaging USP44 variant contributed to the disease in the family we present is not clear. As for the skeletal findings, facial dysmorphism and digestive problems, we did not find a candidate variant. This study is an example of both clinical variation and difficulty in variant detection and evaluation. Our findings highlight that even an extensive exome sequence analysis can fail to fully uncover the complex molecular basis of a syndrome even if potentially causative variants are identified.

Biallelic variants in MAATS1 encoding CFAP91, a calmodulin-associated and spoke-associated complex protein, cause severe astheno-teratozoospermia and male infertility

BackgroundMultiple morphological abnormalities of the flagella (MMAF) consistently lead to male infertility due to a reduced or absent sperm motility defined as asthenozoospermia. Despite numerous genes recently described to be...

Expanding the genotypic spectrum of Jalili syndrome: Novel CNNM4 variants and uniparental isodisomy in a north American patient cohort.

Jalili syndrome is a rare multisystem disorder with the most prominent features consisting of cone-rod dystrophy and amelogenesis imperfecta. Few cases have been reported in the Americas. Here we describe a case series of patients with Jalili syndrome examined at the National Eye Institute’s Ophthalmic Genetics clinic between 2016 and 2018. Three unrelated sporadic cases were systematically evaluated for ocular phenotype and determined to have cone-rod dystrophy with bull’s eye maculopathy, photophobia, and nystagmus. All patients had amelogenesis imperfecta. Two of these patients had Guatemalan ancestry and the same novel homozygous CNNM4 variant (p.Arg236Trp c.706C > T) without evidence of consanguinity. This variant met likely pathogenic criteria by the American College of Medical Genetics guidelines. An additional patient had a homozygous deleterious variant in CNNM4 (c.279delC p.Phe93Leufs*31), which resulted from paternal uniparental isodisomy for chromosome 2p22–2q37. This individual had additional syndromic features including developmental delay and spastic diplegia, likely related to mutations at other loci. Our work highlights the genotypic variability of Jalili syndrome and expands the genotypic spectrum of this condition by describing the first series of patients seen in the United States.

Both rare and common genetic variants contribute to autism in the Faroe Islands

The number of genes associated with autism is increasing, but few studies have been performed on epidemiological cohorts and in isolated populations. Here, we investigated 357 individuals from the Faroe Islands including 36 individuals with autism, 136 of their relatives and 185 non-autism controls. Data from SNP array and whole exome sequencing revealed that individuals with autism had a higher burden of rare exonic copy-number variants altering autism associated genes (deletions (p = 0.0352) or duplications (p = 0.0352)), higher inbreeding status (p = 0.023) and a higher load of rare homozygous deleterious variants (p = 0.011) compared to controls. Our analysis supports the role of several genes/loci associated with autism (e.g., NRXN1, ADNP, 22q11 deletion) and identified new truncating (e.g., GRIK2, ROBO1, NINL, and IMMP2L) or recessive deleterious variants (e.g., KIRREL3 and CNTNAP2) affecting autism-associated genes. It also revealed three genes involved in synaptic plasticity, RIMS4, KALRN, and PLA2G4A, carrying de novo deleterious variants in individuals with autism without intellectual disability. In summary, our analysis provides a better understanding of the genetic architecture of autism in isolated populations by highlighting the role of both common and rare gene variants and pointing at new autism-risk genes. It also indicates that more knowledge about how multiple genetic hits affect neuronal function will be necessary to fully understand the genetic architecture of autism.

FAM46A mutations are responsible for autosomal recessive osteogenesis imperfecta

BackgroundStüve-Wiedemann syndrome (SWS) is characterised by bowing of the lower limbs, respiratory distress and hyperthermia that are often responsible for early death. Survivors develop progressive scoliosis and spontaneous fractures. We...

Mutations in TRAPPC12 Manifest in Progressive Childhood Encephalopathy and Golgi Dysfunction

Progressive childhood encephalopathy is an etiologically heterogeneous condition characterized by progressive central nervous system dysfunction in association with a broad range of morbidity and mortality. The causes of encephalopathy can be either non-genetic or genetic. Identifying the genetic causes and dissecting the underlying mechanisms are critical to understanding brain development and improving treatments. Here, we report that variants in TRAPPC12 result in progressive childhood encephalopathy. Three individuals from two unrelated families have either a homozygous deleterious variant (c.145delG [p.Glu49Argfs∗14]) or compound-heterozygous variants (c.360dupC [p.Glu121Argfs∗7] and c.1880C>T [p. Ala627Val]). The clinical phenotypes of the three individuals are strikingly similar: severe disability, microcephaly, hearing loss, spasticity, and characteristic brain imaging findings. Fibroblasts derived from all three individuals showed a fragmented Golgi that could be rescued by expression of wild-type TRAPPC12. Protein transport from the endoplasmic reticulum to and through the Golgi was delayed. TRAPPC12 is a member of the TRAPP protein complex, which functions in membrane trafficking. Variants in several other genes encoding members of the TRAPP complex have been associated with overlapping clinical presentations, indicating shared and distinct functions for each complex member. Detailed understanding of the TRAPP-opathies will illuminate the role of membrane protein transport in human disease.