OBJECTIVE:This study was the first to identify the biallelic loss-of-function variant in AP1M2 as the cause of autoinflammatory disease with colitis and aimed to elucidate the pathogenesis of AP1M2 deficiency in mice and humans. METHODS:We collected a blood sample and serum sample from a patient for genetic diagnosis and determination of inflammatory cytokines, respectively. Ap1m2-deficient mice on the C57BL/6 background and DLD-1 cells were used to dissect the functional role of Ap1m2 in serum and intestines. Stereo-seq was performed on Ap1m2-/- and Ap1m2-/-::Tnfr1-/- mouse samples to investigate the regulatory role of Tnfr1 signaling in the pathogenesis of Ap1m2 deficiency-caused intestinal inflammation. Superrevolution imaging and clathrin-coated vesicle enrichment were used to explore the molecular mechanism by which AP1M2 suppresses NF-κB activation and chemokine production. RESULTS:Ap1m2-/- mice exhibited elevated chemokine production in serum and spontaneously developed intestinal inflammation, which phenocopies the patient with the AP1M2 variant. Mechanistically, the deficiency of intestinal epithelial specific AP1M2 expression resulted in accumulation of TNFR1-signaling downstream proteins, including RIPK1, TBK1, IKKα/β, and NEMO, leading to enhanced NF-κB activation and subsequent chemokine overproduction. Tnfr1 knockout rescued gastrointestinal inflammation induced by Ap1m2 deficiency through suppressing NF-κB activation and chemokine production. CONCLUSION:This study identifies the deficiency of AP1M2 as the cause of a new autoinflammatory disease with colitis and highlights the critical function of AP-1 in suppressing NF-κB activation and chemokine production.

Supplementary Figure S1: Study design for the evaluation of FS118 in subjects with advanced solid tumors whoprogressed on or after prior PD-(L)1 therapy.Supplementary Figure S2: Time on FS118 treatment in patients with primary or acquired resistance to prioranti-PD-(L)1 therapies.Supplementary Figure S3: Total time on prior ICB therapies compared to the timeon FS118 treatment in patients with primary or acquired resistance to prior antiPD-(L)1 therapies.Supplementary Figure S4: Levels of soluble LAG-3 (sLAG-3) detected inthe serum of patients in the FS118 phase 1 trial.Supplementary Figure S5: Changes in circulating immune cells in FS118-treated patients.

To date, the KCTD10 gene (MIM: 608726) has not been definitively associated with a human disease, although studies in animal models suggest that it plays a role in embryonic development. We have identified multiple unrelated individuals with de novo missense variants and overlapping phenotypes, including congenital heart anomalies and congenital anomalies in other organ systems, in our internal database. This report includes a detailed description of the genotype and phenotype for two consented individuals and aggregate data of additional individuals who were not available for case-specific publication. Based on the data presented here, we propose that damaging de novo missense KCTD10 variants are associated with an autosomal dominant phenotype that includes cardiac and other congenital anomalies. We encourage additional studies to further characterize this condition and identify a mechanism for disease.

Tumor-infiltrating lymphocytes (TILs) often have upregulated expression of immune checkpoint receptors, such as programmed cell death 1 (PD-1) and lymphocyte-activation gene 3 (LAG-3). Patients treated with antibodies targeting PD-1 or its ligand (PD-L1) can develop resistance or relapse, with LAG-3 upregulation on T cells being one possible mechanism. FS118 is a tetravalent, bispecific antibody comprising a full-length IgG 1 anti-PD-L1 antibody with bivalent LAG-3-binding capability in the fragment crystallizable region. Here we demonstrate how the structure of FS118 is important for its function. We generated variants of FS118 and tested their ability to mediate LAG-3 shedding using staphylococcal enterotoxin B assays, antigen recall assays, and soluble LAG-3 ELISAs. Mediated by metalloproteases ADAM10 and ADAM17, FS118 induced shedding of LAG-3 from the surface of both CD4 + and CD8 + T cells. We also determined the effect of surrogate antibodies on immune cell LAG-3 expression and proliferation in syngeneic mouse models. In vivo , the bivalent LAG-3 binding sites of a mouse surrogate of FS118 and their location in the fragment crystallizable region were important for eliciting maximal reduction in LAG-3 levels on the surface of TILs, as variants with a single LAG-3 binding site in the fragment crystallizable region, or with reversed orientation of the LAG-3 and PD-L1 binding sites, were less efficient at inducing shedding. We also show that PD-L1, not PD-1, binding drives the LAG-3 reduction on TILs. We hypothesize that the LAG-3 bivalency in the fragment crystallizable region of FS118 allows LAG-3 clustering, which optimizes cleavage by ADAM10/ADAM17 and thus shedding.

Innovative and easy-to-implement strategies are needed to improve the pathogenicity assessment of rare germline missense variants. Somatic cancer driver mutations identified through large-scale tumor sequencing studies often impact genes that are also associated with rare Mendelian disorders. The use of cancer mutation data to aid in the interpretation of germline missense variants, regardless of whether the gene is associated with a hereditary cancer predisposition syndrome or a non-cancer-related developmental disorder, has not been systematically assessed. We extracted putative cancer driver missense mutations from the Cancer Hotspots database and annotated them as germline variants, including presence/absence and classification in ClinVar. We trained two supervised learning models (logistic regression and random forest) to predict variant classifications of germline missense variants in ClinVar using Cancer Hotspot data (training dataset). The performance of each model was evaluated with an independent test dataset generated in part from searching public and private genome-wide sequencing datasets from ~1.5 million individuals. Of the 2,447 cancer mutations, 691 corresponding germline variants had been previously classified in ClinVar: 426 (61.6%) as likely pathogenic/pathogenic, 261 (37.8%) as uncertain significance, and 4 (0.6%) as likely benign/benign. The odds ratio for a likely pathogenic/pathogenic classification in ClinVar was 28.3 (95% confidence interval: 24.2-33.1, p < 0.001), compared with all other germline missense variants in the same 216 genes. Both supervised learning models showed high correlation with pathogenicity assessments in the training dataset. There was high area under precision-recall curve values (0.847 and 0.829) and area under the receiver-operating characteristic curve values (0.821 and 0.774) for logistic regression and random forest models, respectively, when applied to the test dataset. With the use of cancer and germline datasets and supervised learning techniques, our study shows that cancer mutation data can be leveraged to improve the interpretation of germline missense variation potentially causing rare Mendelian disorders.

Supplementary Table S1: Representativeness of Study Participants.Supplementary Table S2: Immunogenicity in patients treated with FS118.Supplementary Table S3: PK of FS118 by Dose Level.

Introduction Agonists of CD137, a co-stimulatory receptor expressed on activated lymphocytes, are under investigation, including their use in combination with immune checkpoint blockade. FS222 is a tetravalent bispecific antibody targeting both CD137 and programmed death-ligand 1 (PD-L1).Methods Fragment crystallizable regions with antigen-binding (Fcab (TM)) domains with high avidity to CD137 were engineered and matured. A resulting Fcab was introduced into a human high-affinity PD-L1 monoclonal antibody, generating FS222. Valency variants of FS222 and its mouse surrogate (FS222m) were generated. Antibody properties were assessed in vitro, while antitumor efficacy and T-cell proliferation were evaluated in vivo.Results FS222 could bind to two copies of each antigen concurrently ('2+2' binding). In T-cell activation assays, FS222 and a variant that is bivalent for CD137 and monovalent for PD-L1 activated T cells, whereas monovalent variants for CD137 did not. FS222 had no hook effect up to 300 nM and was superior to a heterodimeric '1+1' CD137/PD-L1 bispecific antibody. In mixed lymphocyte reaction assays, FS222 and another bivalently linked antibody for PD-L1 were more potent than monovalent antibodies for PD-L1. In syngeneic mouse models, FS222m was associated with more peripheral T-cell proliferation and antitumor efficacy than all MC38 or most CT26.WT valency variants.Discussion FS222 could potently target and activate high CD137-expressing tumor-infiltrating lymphocytes due to its high avidity for CD137. FS222 demonstrates activity when PD-L1 levels are limited, highlighting its potential activity in tumors insensitive to PD-1 blockade, and in situations requiring both PD-L1 and CD137 binding. This may have clinical relevance.Conclusion In this study, it was found that the '2+2' structure of FS222 is superior to that of a '1+1' CD137/PD-L1 antibody.

The ARHGEF40 gene, also known as SOLO, encodes a RhoA-targeting guanine nucleotide exchange factor (GEF) and is currently considered a candidate gene with a potential relationship to disease. Our laboratory has confirmed variants at position p.Arg225 of the ARHGEF40 protein in multiple unrelated individuals with a phenotype including dysmorphic features, congenital anomalies and neurodevelopmental abnormalities. Here, we provide genetic and phenotypic information for two individuals harboring de novo variants at p.Arg225 and sharing a highly similar phenotype. This report suggests a relationship between variants at this amino acid position and autosomal dominant disease, and further studies will be needed to characterize this disease-gene relationship and elucidate the disease mechanism.

PurposeTo determine the degree to which likely causal missense variants of single-locus traits in domesticated species have features suggestive of pathogenicity in a human genomic context.MethodsWe extracted missense variants from the Online Mendelian Inheritance in Animals database for nine animals (cat, cattle, chicken, dog, goat, horse, pig, rabbit and sheep), mapped coordinates to the human reference genome and annotated variants using genome analysis tools. We also searched a private commercial laboratory database of genetic testing results from >400 000 individuals with suspected rare disorders.ResultsOf 339 variants that were mappable to the same residue and gene in the human genome, 56 had been previously classified with respect to pathogenicity: 31 (55.4%) pathogenic/likely pathogenic, 1 (1.8%) benign/likely benign and 24 (42.9%) uncertain/other. The odds ratio for a pathogenic/likely pathogenic classification in ClinVar was 7.0 (95% CI 4.1 to 12.0, p<0.0001), compared with all other germline missense variants in these same 220 genes. The remaining 283 variants disproportionately had allele frequencies and REVEL scores that supported pathogenicity.ConclusionCross-species comparisons could facilitate the interpretation of rare missense variation. These results provide further support for comparative medical genomics approaches that connect big data initiatives in human and veterinary genetics.

Selenophosphate synthetase (SEPHS) plays an essential role in selenium metabolism. Two mammalian SEPHS paralogues, SEPHS1 and SEPHS2, share high sequence identity and structural homology with SEPHS. Here, we report nine individuals from eight families with developmental delay, growth and feeding problems, hypotonia, and dysmorphic features, all with heterozygous missense variants in SEPHS1. Eight of these individuals had a recurrent variant at amino acid position 371 of SEPHS1 (p.Arg371Trp, p.Arg371Gln, and p.Arg371Gly); seven of these variants were known to be de novo. Structural modeling and biochemical assays were used to understand the effect of these variants on SEPHS1 function. We found that a variant at residue Trp352 results in local structural changes of the C-terminal region of SEPHS1 that decrease the overall thermal stability of the enzyme. In contrast, variants of a solvent-exposed residue Arg371 do not impact enzyme stability and folding but could modulate direct protein-protein interactions of SEPSH1 with cellular factors in promoting cell proliferation and development. In neuronal SH-SY5Y cells, we assessed the impact of SEPHS1 variants on cell proliferation and ROS production and investigated the mRNA expression levels of genes encoding stress-related selenoproteins. Our findings provided evidence that the identified SEPHS1 variants enhance cell proliferation by modulating ROS homeostasis. Our study supports the hypothesis that SEPHS1 plays a critical role during human development and provides a basis for further investigation into the molecular mechanisms employed by SEPHS1. Furthermore, our data suggest that variants in SEPHS1 are associated with a neurodevelopmental disorder.

De novo variants adjacent to the canonical splicing sites or in the well-defined splicing-related regions are more likely to impair splicing but remain under-investigated in autism spectrum disorder (ASD). By analyzing large, recent ASD genome sequencing cohorts, we find a significant burden of de novo potential splicing-disrupting variants (PSDVs) in 5048 probands compared to 4090 unaffected siblings. We identified 55 genes with recurrent de novo PSDVs that were highly intolerant to variation. Forty-six of these genes have not been strongly implicated in ASD or other neurodevelopmental disorders previously, including GSK3B. Through international, multicenter collaborations, we assembled genotype and phenotype data for 15 individuals with GSK3B variants and identified common phenotypes including developmental delay, ASD, sleeping disturbance, and aggressive behavior. Using available single-cell transcriptomic data, we show that GSK3B is enriched in dorsal progenitors and intermediate forms of excitatory neurons in the developing brain. We showed that Gsk3b knockdown in mouse excitatory neurons interferes with dendrite arborization and spine maturation which could not be rescued by de novo missense variants identified from affected individuals. In summary, our findings suggest that PSDVs may play an important role in the genetic etiology of ASD and allow for the prioritization of new ASD candidate genes. Importantly, we show that genetic variation resulting in GSK3B loss-of-function can lead to a neurodevelopmental disorder with core features of ASD and developmental delay.

BACKGROUND:Biallelic ZBTB11 variants have previously been associated with an ultrarare subtype of autosomal recessive intellectual developmental disorder (MRT69). OBJECTIVE:The aim was to provide insights into the clinical and genetic characteristics of ZBTB11-related disorders (ZBTB11-RD), with a particular emphasis on progressive complex movement abnormalities. METHODS:Thirteen new and 16 previously reported affected individuals, ranging in age from 2 to 50 years, with biallelic ZBTB11 variants underwent clinical and genetic characterization. RESULTS:All patients exhibited a range of neurodevelopmental phenotypes with varying severity, encompassing ocular and neurological features. Eleven new patients presented with complex abnormal movements, including ataxia, dystonia, myoclonus, stereotypies, and tremor, and 7 new patients exhibited cataracts. Deep brain stimulation was successful in treating 1 patient with generalized progressive dystonia. Our analysis revealed 13 novel variants. CONCLUSIONS:This study provides additional insights into the clinical features and spectrum of ZBTB11-RD, highlighting the progressive nature of movement abnormalities in the background of neurodevelopmental phenotype.

The post-transcriptional modification of tRNAs plays a key role in tRNA folding and function to ensure proper levels of protein synthesis during growth and development. Pathogenic variants in tRNA modification enzymes have been implicated in diverse human neurodevelopmental and neurological disorders. However, the molecular basis for many of these disorders remains unknown, thereby limiting our understanding and potential treatment of pathologies linked to tRNA modification. Here, we describe an extensive cohort of 31 individuals from 24 unrelated families with bi-allelic variants in the tRNA methyltransferase 1 ( TRMT1 ) gene who present with a syndromic neurodevelopmental disorder universally characterized by intellectual disability in affected patients. Developmental delay, behavioral abnormalities and facial dysmorphisms represent additional core phenotypes of this syndrome. The variants include novel and ultra-rare TRMT1 variants that segregate with clinical pathology. We found that a subset of variants causes mis-splicing and loss of TRMT1 protein expression. Notably, patient cells with TRMT1 variants exhibit a deficiency in tRNA modifications catalyzed by TRMT1. Molecular analysis of TRMT1 variants reveal distinct regions of the TRMT1 protein required for tRNA modification activity and binding, including a TRMT1 subdomain critical for tRNA interaction. Importantly, depletion of TRMT1 in zebrafish is sufficient to induce developmental and behavioral phenotypes that recapitulate those observed in human patients with pathogenic TRMT1 variants. Altogether, these findings demonstrate that loss of TRMT1-catalyzed tRNA modifications leads to a syndromic form of intellectual disability and elucidate the molecular underpinnings of tRNA modification deficiency caused by pathogenic TRMT1 variants. ### Competing Interest Statement M.M.M and A.C are employees of GeneDx, LLC. R.S. is on the advisory board for Guide Genetics and Egetis Pharmaceuticals. ### Funding Statement The research in this manuscript was supported by NIH GR530882 to D.F. Studies performed in the lab of G.K.V was funded by NIH R24OD034438. The clinic-genetic research was funded in part, by the Wellcome Trust (WT093205MA, WT104033AIA). This study was funded by the Medical Research Council (MR/S01165X/1, MR/S005021/1, G0601943), The National Institute for Health Research University College London Hospitals Biomedical Research Centre, Rosetrees Trust, Ataxia UK, Multiple System Atrophy Trust, Brain Research United Kingdom, Sparks Great Ormond Street Hospital Charity, Muscular Dystrophy United Kingdom (MDUK), Muscular Dystrophy Association (MDA USA) and the King Baudouin Foundation. SE and HH were supported by an MRC strategic award to establish an International Centre for Genomic Medicine in Neuromuscular Diseases (ICGNMD) MR/S005021/1. B.V. was supported by the Deutsche Forschungsgemeinschaft (DFG) DFG VO 2138/7‐1 grant 469177153. J.S. is supported by Cancer Research UK and University College London. A.F. and S.C. are supported by Health & Care Research Wales, Epilepsy Research UK, PhD Swansea University funding. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The accredited Medical Ethics Review Committee of the University College London Hospital, as well as all collaborating local institutional IRBs have approved the collection of biomaterial samples and clinical information as well as functional analysis of human DNA and fibroblasts. The patients and their families provided informed consent for participation in the study and publication of the results. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.

Interpreting rare missense variants is a major challenge in human genetics. Existing in silico prediction tools often consider evolutionary conservation of a residue. However, the correlation between disease associations of specific variants across species is not well characterized. We hypothesized that for variants causing Mendelian disease in non-human livestock and domestic species, the orthologous variant would be similarly functionally significant in humans.

MGA (OMIM: 616061) encodes a dual-specificity transcription factor that regulates the expression of Max-network and T-box family target genes, important in embryogenesis. Previous studies have linked MGA to various phenotypes, including neurodevelopmental disorders, congenital heart disease, and early-onset Parkinson's disease. Here, we describe the clinical phenotype of individuals with de novo, heterozygous predicted loss-of-function variants in MGA, suggesting a unique disorder involving both neurodevelopmental and congenital anomalies. In addition to developmental delays, certain congenital anomalies were present in all individuals in this cohort including cardiac anomalies, male genital malformations, and craniofacial dysmorphisms. Additional findings seen in multiple individuals in this cohort include hypotonia, abnormal brain imaging, hearing loss, sleep dysfunction, urinary issues, skeletal abnormalities, and feeding difficulties. These findings provide support for MGA as a gene intolerant to protein truncation with a broad phenotypic spectrum.