Spliceosomopathies are syndromes caused by pathogenic variants in genes involved in splicing and mRNA metabolism. Here, we report a novel spliceosomopathy caused by de novo variants in SF3B3, encoding a subunit of the spliceosomal SF3b complex. We performed genomic, clinical, computer-aided gestalt analysis, molecular dynamics simulations, and functional studies using patient-derived fibroblasts. Through international data sharing, we collected clinical and molecular data from 24 unrelated individuals with heterozygous SF3B3 variants, mostly missense, consistent with autosomal dominant inheritance. Individuals exhibited a congruent phenotype including autism spectrum disorder (ASD), developmental delay (DD), intellectual disability (ID), language and motor delay, multiple congenital anomalies, and distinctive craniofacial features, confirmed by GestaltMatcher analysis. In patient fibroblasts, SF3B3 mRNA was within the normal range, whereas protein levels were reduced by approximately 15–30

Congenital insensitivity to pain (CIP) refers to a group of extremely rare genetic disorders characterized by a lifelong inability to sense pain. Interestingly, in most cases, other neurological functions remain essentially intact. Here, we present the long-term follow-up of a 73 year old Icelandic male who, along with his two brothers, were diagnosed with CIP in childhood. This report details his clinical history, neurological findings, and whole genome sequencing results, which confirm and elucidate the genetic basis of his condition, explained by compound heterozygosity of two rare mutations in SCN9A. One has previously been described in CIP (p.Lys1659Ter). The other is a novel CIP variant consisting of a rare deletion (c.417-15_4174-14delAT) that causes exon 23 to be spliced out, and loss of 18 amino acids from the protein.

WD and tetratricopeptide repeats protein 1 (WDTC1) encodes a component of the cullin-RING E3 ligase complexes that mediate polyubiquitination of specific target proteins for degradation and has been shown to regulate lipid storage in studies performed in Drosophila, mice, and humans. WDTC1 is expressed in a wide variety of tissues and organs including the brain and is predicted to be loss-of-function intolerant. To determine the phenotypes associated with WDTC1 haploinsufficiency, we identified seven individuals, six of whom have not been previously reported, who are heterozygous for loss-of-function or putatively damaging missense variants in WDTC1. None of these individuals were reported to be obese, but all had neurodevelopmental phenotypes that included developmental delay and intellectual disability. Seizures were also recurrently reported. One loss-of-function variant was inherited from an affected mother, and one missense variant was inherited from an unaffected father. Our findings suggest that WDTC1 haploinsufficiency causes a neurodevelopmental syndrome characterized by variable developmental delay, intellectual disability, and seizures. The identification of additional patients with loss-of-function variants will be needed to identify recurrent patterns of less common phenotypes, determine with greater certainty if obesity is or is not a feature associated with this disorder, and confirm that this disorder is incompletely penetrant.

High fetal hemoglobin level is the most important predictor of favorable clinical outcome in sickle cell disease. We carried out a genome-wide association study (GWAS) on estimated fetal beta globin RNA expression ratio (FGR) using blood RNA sequence data from 22,093 adult Icelanders. In addition to the well-known BCL11A, HBB/HBG2 and HBS1L-MYB loci, we found 33 loci associated with FGR conditioned on variants at these 3 loci (cFGR). We identified fourteen candidate causal genes at the 33 loci. In the ZBTB7A, GFI1B, ZFPM1, and ALAS2 genes we identified rare loss-of-function variants that associate with large effect on cFGR. A rare variant in ZBTB7A, which had the largest increasing effect on cFGR, generates an alternative upstream inframe ATG in an erythroid specific transcript encoding an addition of 119 amino acids to the protein, highlighting a potential therapeutic target. Furthermore, rare variants with large effects in ALAS2 and GFI1B implicate the heme biosynthesis pathway and isoform specific role of GFI1B in fetal hemoglobin regulation.

Muscle mass is central to physical function and metabolic health 1 , but can decrease with disease, aging 2 and weight loss interventions 3-5 . As such interventions become more widely used, agents that preserve or increase muscle mass are needed. To identify such therapeutic opportunities, we performed genome-wide association meta-analyses (GWAS) of arm, leg, trunk and total lean mass measured by dual-energy X-ray absorptiometry (DXA), a widely used method to estimate muscle mass. We identified 63 loci, including the rare missense variant in MSTN (p.Ile225Thr, rs143242500), which had the largest effect on leg lean mass (β = 0.28 SD [95% CI: 0.19, 0.37], P = 1.9 × 10 -9 ). MSTN encodes myostatin, a negative regulator of skeletal muscle mass and a therapeutic target for muscle wasting disorders 6 . p.Ile225Thr is the first genome-wide significant association in MSTN in humans with functional consequences and could provide further insight into long-term systemic effects of myostatin inhibition.

BACKGROUND:We aimed to characterize the genetic architecture of resistant hypertension (rHTN), which affects up to 18% of hypertensive individuals and increases cardiovascular disease risk. METHODS:We conducted a genome-wide association study on rHTN, defined as use of 3 or more concomitant antihypertensive drugs for at least 6 months without reaching blood pressure target (in the 3-drug case), comparing it to controlled hypertension (cHTN), in which persons on 1 or 2 antihypertensives for at least 6 months reach target BP after 30 days of therapy initiation. The study included 23 508 rHTN cases and 24 393 cHTN controls, identified through drug prescription and blood pressure data from Iceland (deCODE), the UK (UK Biobank), and the US (eMERGE). Further analyses included comparisons with all hypertensive individuals (diagnosed with International Classification of Diseases, Tenth Revision code I10) and normotensives (no hypertension diagnosis). RESULTS:We found 24 rHTN variants, 17 of which used published BP variants as prior. Fifteen risk-increasing rHTN alleles are associated with lower serum potassium and increased hyperaldosteronism risk. Individuals with rHTN and cHTN had lower potassium levels before drug therapy than normotensives. All antihypertensive drug classes increased potassium levels in cHTN, while only aldosterone antagonists increased levels in rHTN. Mendelian randomization analysis was consistent with rHTN being a manifestation of hyperaldosteronism. The variant conferring the largest effect on both rHTN and hyperaldosteronism is a stop-gain variant in ENPEP in the aldosterone pathway. CONCLUSIONS:We discovered sequence variants that have different effects on rHTN and cHTN. Our study indicates that genetically determined hyperaldosteronism may be largely accountable for rHTN.

Intrahepatic cholestasis of pregnancy, which affects 0.2-2% of pregnancies, is characterized by pruritus, increased aminotransferase activity and elevated serum bile acids. Previous studies have implicated liver-enriched genes in intrahepatic cholestasis of pregnancy. We conducted a meta-analysis of intrahepatic cholestasis of pregnancy genome-wide association studies in the FinnGen study, deCODE, Estonian Biobank, the Danish Blood Donor Study and Copenhagen Hospital Biobank with 4,738 women with prior ICP and 436,834 female controls. The analysis found 26 genome-wide significant associations of which 10 were novel. Genes in the associated loci were prioritized using lead SNP expression quantitative trait loci associations and colocalization analysis to assess potential causality. The associated loci implicate bile acid synthesis, LDL cholesterol, and lipid metabolism. Additionally, comorbidity, genetic correlation and polygenic risk score analyses further indicated a link between intrahepatic cholestasis of pregnancy and pancreatitis, suggesting shared genetic underpinnings.

Short Abstract Emerging evidence indicates that oral and systemic health are interconnected, yet the basis of this relationship remains incompletely understood. In a genome-wide association study of objectively measured dental caries in permanent dentition among Danish children and adolescents (DC CA ) (N = 151,521), we identified 14 independent loci. Genes at DC CA -associated loci were enriched for expression in immune, secretory and epithelial cell populations. We found genetic correlations and evidence for shared causal variants with several cardiometabolic traits. Leveraging data from UK Biobank (N max = 501,936) and independent pediatric cohorts (N max = 3,412), we showed that genetic liability to DC CA associated with dentures, risk of coronary artery disease and type 2 diabetes in adults, and with HbA1C, lipid, liver enzyme levels, and plasma proteins implicated in oral, metabolic and hepatic biology in both populations. Our results provide new insights into the genetic architecture underlying the relationship between DC CA and cardiometabolic disease.

LRP1 encodes the low-density lipoprotein (LDL) receptor-related protein 1 (LRP1), a transmembrane protein involved in endocytosis and activation of multiple signaling pathways. LRP1 variants have been implicated in the pathogenesis of congenital heart defects (CHD), Alzheimer's disease, and neurodevelopmental disorders (NDD). Biallelic LRP1 variants have also been reported in two siblings with CHD, hypotonia, dysmorphology, corneal clouding, and ascites. However, conclusive evidence supporting the role of LRP1 in human disease is still lacking. Individuals with heterozygous variants in LRP1 (NM_002332.3) were identified through genetic testing. GeneMatcher facilitated identification of participants and international collaboration. Comprehensive clinical and genotypic data were collected. Fifteen participants with heterozygous predicted loss-of-function (pLOF) or missense variants in LRP1 were identified. The most common phenotypes include NDD, CHD, musculoskeletal and gastrointestinal issues, and dysmorphic features. CHD was more common in participants with pLOF variants. Our findings suggest that LRP1 haploinsufficiency is associated with a syndromic NDD. Phenotypic differences in cardiac and neurologic involvement between participants with pLOF and missense variants suggest the possibility of alternate disease mechanisms.

SF3B1 is an essential and ubiquitous splicing factor that plays a pivotal role in the early steps of pre-mRNA splicing. Recurrent somatic missense mutations in SF3B1 are frequent in cancers, but no constitutional variant has been reported so far. We describe here a cohort of 26 individuals with neurodevelopmental disorders, harbouring SF3B1 constitutional heterozygous variants that appeared mostly de novo. Patients present with a global developmental delay, associated with variable neurological and facial dysmorphic traits. A dichotomy may emerge between patients harbouring predicted loss of function (n = 9) and missense variants (n = 17), the latter being associated with a more severe and syndromic phenotype, including heart and gastrointestinal anomalies. We focused on de novo SF3B1 missense variants, which were largely distinct from those reported in cancer. Functional complementation assays show that de novo SF3B1 missense variants did not cause a loss of function of the protein. Targeted and genome-wide analysis of RNA splicing reveal that they affect canonical and alternative splicing more moderately than somatic variants, and subtly modify the splicing of many transcripts. These findings place SF3B1 among the rare U2 snRNP components implicated in both cancer and neurodevelopmental disorders, highlighting its critical and multifaceted role in human disease. This study reports that de novo germline missense variants in SF3B1, distinct from the somatic variants frequently observed in cancer, cause a neurodevelopmental disorder and disrupt global RNA splicing.

ABSTRACT Genome-wide association studies have linked thousands of sequence variants to immune-mediated diseases, yet their cellular mechanisms remain largely unresolved. Here we present BloodVariome, a high-resolution atlas of genetic effects across the human immune cell hierarchy. Combining deep immunophenotyping with automated pattern-recognition, we quantified 1,533 traits across 127 immune cell populations in 11,983 individuals. We identified 259 significant associations, the vast majority of which are not captured by conventional bulk blood trait studies. Most associations were restricted to single immune lineages or cell populations, revealing a fine-grained genetic compartmentalization of the immune system. By linking known disease risk alleles to specific immune cell phenotypes, BloodVariome illuminates cellular mechanisms underlying autoimmunity, immunodeficiency, and hematologic malignancy. Moreover, we implicate novel regulators of human immune cell development and function. By bridging the gap between cohort size and phenotypic depth, BloodVariome establishes a high-resolution framework for interpreting how genetic variation shapes cellular immunity at population-scale.

Fibromyalgia is a common and debilitating chronic pain syndrome of poorly understood etiology. Here, we conduct a multi-ancestry genome-wide association study meta-analysis across 2,563,755 individuals (54,629 cases and 2,509,126 controls) from 11 cohorts, identifying the first 26 risk loci for fibromyalgia. The strongest association was with a coding variant in HTT, the causal gene for Huntington's disease. Gene prioritization implicated the HTT regulator GPR52, as well as diverse genes with neural roles, including CAMKV, DCC, DRD2/NCAM1, MDGA2, and CELF4. Fibromyalgia heritability was exclusively enriched within brain tissues and neural cell types. Fibromyalgia showed strong, positive genetic correlation with a wide range of chronic pain, psychiatric, and somatic disorders, including genetic correlations above 0.7 with low back pain, post-traumatic stress disorder and irritable bowel syndrome. Despite large sex differences in fibromyalgia prevalence, the genetic architecture of fibromyalgia was nearly identical between males and females. This work provides the first robust genetic evidence defining fibromyalgia as a central nervous system disorder, thereby establishing a biological framework for its complex pathophysiology and extensive clinical comorbidities.

Germline mutations are heritable; they occur before the formation of a fertilized egg and are found in all cells. They can be detected through somatic tissue sampling, and de novo mutations (DNMs) are well-studied. The majority of known DNMs originate in paternal cells, but some include maternal contributions as well. Certain kinds of DNMs prevent a fertilized egg from developing to term, and these are much less well-characterized. Some also lack sequence variants in certain genes and some are never observed in a homozygous form; these are also not well studied. Recombination failure can cause aneuploidies (trisomies or monosomies), and an estimated half of pregnancy losses are explained by this phenomenon. Early pregnancy loss is understudied, and there are few therapeutic interventions. This study, the Copenhagen Pregnancy Loss (COPL) study, was designed to contribute to the understanding of pregnancy loss through trios of patients (mother, father, and fetus) with clinically diagnosed pregnancy loss, attempting to document sequence diversity and interplay between meiotic recombination and point mutations. This study included 664 cases of early pregnancy loss with 1439 fetal samples (multiple were collected from each loss, where possible). In 467 of the 664 cases, there was at least 1 fetal sample and 1 sample from both parents. A total of 59 losses indicated a higher-than-expected kinship with the mother, and 11 indicated a higher kinship with the father. Whole-genome sequencing (WGS) was used to assess aneuploidies, and detected them in 206 cases. Of these, monosomy X and trisomy 16 were the most common. In addition, 19 large de novo copy number variants (CNVs) were detected in 14 loss cases, none of which were near a common fragile site. Of these 14 cases, 11 were euploid losses and 6 contained aneuploidies. Failure at meiosis I results in the presence of both homologous chromosomes from the same parent. An estimated 27.2% of paternal and 32.3% of maternal triploidies occur at recombination hotspots, supporting the idea of meiosis failure. A total of 15,086 DNMs were pinpointed as paternal and 5967 as maternal, consistent with previous literature supporting a high paternal contribution to DNMs. Consistent with this, paternal triploidies showed a proportionally higher paternal fraction of phased mutations. DNMs shown in maternal triploidies indicated a lower paternal fraction than euploid fetuses. In addition, there was no correlation between sister/homologous state differences for high-AB DNMs in paternal triploidies. When searching for pathogenic single-site variants (SSVs) in the DNMs, 26 genotypes were found that were pathogenic or likely pathogenic; a total of 23 were DNMs and 3 were biallelic predicted loss-of-function variants (pLoF). The frequency of pathogenic SSVs in early pregnancy loss was higher compared with controls [odds ratio (OR) 2.98, P=5.7×10-6), and this effect remained after correction for parental age. These results showed probable genetic causes for pregnancy loss in 254 of 467 cases, including aneuploidies, triploidies, pathogenic SSVs, and de novo CNVs. Most of the genetic causes of loss originated on maternal chromosomes, and fetuses with triploidies had significantly more DNMs than fetuses that were euploid. These results indicate significant sequence diversity in early pregnancy loss, with additional diversity likely present but unidentified in the stages between implantation and clinically recognized pregnancy. Future research should focus on potential explanations for early pregnancy loss that cannot be explained by genetic causes, as well as on potential interventions for these cases.

The causal effect of lower plasma sclerostin on cardiovascular disease (CVD) risk has previously been examined with the aim of investigating potential side effects of pharmacological sclerostin inhibition for treatment of osteoporosis. We explored the relationship between plasma sclerostin levels and CVDs and bone phenotypes using Mendelian randomization (MR) and correlation between plasma sclerostin levels and these outcomes. We used variants identified in genome-wide association studies of plasma sclerostin levels in large proteomic datasets from the UK Biobank (Olink) and Iceland (SomaScan) as instruments in two separate MR analyses. These analyses did not provide evidence of association between the effects of sequence variants on plasma sclerostin levels and their effects on CVDs and CVD risk factors (P > 0.05). Several of the instruments had heterogenic effects on bone phenotypes and causal estimates in MR were non-significant (P > 0.05/8). Plasma sclerostin levels correlated positively with coronary artery disease, myocardial infarction and CVD risk factors. Our results do not provide evidence supporting the hypothesis that lower plasma sclerostin levels increase CVD risk and suggest that plasma sclerostin levels are not a good surrogate for pharmacological inhibition.

Small nuclear RNAs (snRNAs) combine with specific proteins to generate small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. U4 snRNA forms a duplex with U6 and, together with U5, contributes to the tri-snRNP spliceosomal complex. Variants in RNU4-2, which encodes U4, have recently been implicated in neurodevelopmental disorders. Here we show that heterozygous inherited and de novo variants in RNU4-2 and in four RNU6 paralogs (RNU6-1, RNU6-2, RNU6-8 and RNU6-9), which encode U6, recur in individuals with nonsyndromic retinitis pigmentosa (RP), a genetic disorder causing progressive blindness. These variants cluster within the three-way junction of the U4/U6 duplex, a site that interacts with tri-snRNP splicing factors also known to cause RP (PRPF3, PRPF8, PRPF31), and seem to affect snRNP biogenesis. Based on our cohort, deleterious variants in RNU4-2 and RNU6 paralogs may explain up to ~1.4% of otherwise undiagnosed RP cases. This study highlights the contribution of noncoding RNA genes to Mendelian disease and reveals pleiotropy in RNU4-2, where distinct variants underlie neurodevelopmental disorder and retinal degeneration.

Reference bias is an issue that affects most genomic studies analysing short reads mapped to a reference genome1,2. It can be mitigated by mapping to multiple haplotypes represented in a pangenome3-5. Here we introduce two new methods to address reference bias: Emblask for pangenome construction and Weaver for mapping to pangenomes at scale. Emblask is a hybrid long- and short-read haplotype-resolved dual assembly pipeline for parent-offspring trio data. Using Emblask, we assembled 698 Icelandic haplotypes and added them to the Human Pangenome Reference Consortium (HPRC) pangenome4 to construct an Icelandic pangenome reference (HPRC-ICE) including 51.41 million small variants. We mapped the short reads of 57,630 Icelanders to HPRC-ICE with Weaver and called 98.96 million variants, representing a 6.17% increase over mapping to a linear reference. We uncovered new variants in low-mappability regions, including a pathogenic single nucleotide polymorphism (SNP) in GBA1 that associates with early onset Parkinson's disease and a missense SNP in CBS that is pathogenic for homocystinuria. We replicated the GBA1 association in the UK Biobank6 with a targeted remapping of 429,193 British and Irish participants.

ABSTRACT Immunoglobulins (Ig) mediate adaptive humoral immunity, yet the regulation of B-cell responses in vivo in humans remains inaccessible to direct experimentation. Here we use population-scale Ig genetics to resolve molecular regulation of the human B-cell system. Analysis of circulating IgA, IgG, IgM, and six composite Ig traits in 114,697 individuals identifies 504 genetic associations. Integration with regulatory genomics, plasma proteomics, and immunophenotyping maps these effects across the B-cell hierarchy, recovering known regulators and revealing previously unrecognized genes in humoral immunity. At key control nodes – including Fcγ receptors, the immunoglobulin heavy-chain locus and the TACI–APRIL signaling axis – variants form allelic series generating graded perturbations of antibody output. Ig-associated loci show extensive overlap with autoimmunity, immunodeficiency and B-cell malignancy. These findings demonstrate that Ig traits, analyzed at population scale, encode fine-grained information about the regulation of the human B-cell system and link natural variation in humoral immunity to immune-mediated disease.

Cutaneous lupus erythematosus (CLE) is an autoimmune disease of the skin, occurring with or without systemic lupus erythematosus (SLE). People with African ancestry have a higher risk than people with other ancestries of developing lupus1 but have been underrepresented in genetic studies. We whole-genome-sequenced 27,820 Americans with genetically inferred African ancestry from the Diverse Ancestry Cohort, including people with CLE (n = 211) and/or SLE (n = 574). We discovered an association with a rare missense variant in IKBKB, rs115698972G>A, IKKβE502K, exclusive to people with African ancestry, conferring an odds ratio (OR) of 5.4 for CLE and 3.3 for SLE. These associations replicated in the All of Us and VA Million Veteran Research Programs for CLE (ORmeta = 3.8, Pmeta = 5.3 × 10-20, n = 1,243) and SLE (ORmeta = 3.2, Pmeta = 1.0 × 10-19, n = 1,697). In this cohort, IKKβE502K accounts for 10.4% of CLE cases and 6.4% of SLE cases, confers a high lupus risk, and contributes substantially to the disease prevalence among people with African ancestry. This highlights the value of including diverse ancestries in genetic association studies.

Background & Aims:The genetic underpinnings of hepatocellular carcinoma (HCC) remain largely unknown. Thus, we aimed to identify new genetic risk loci for HCC. Methods:We performed a genome-wide association study (GWAS) meta-analysis of 11 cohorts with validation in two independent cohorts. The identified variants were tested for effects on other hepatobiliary endpoints, and on incident HCC stratified by underlying risk factors. Mendelian randomization was used to assess the causal effects of a range of traits on the risk of HCC. Results:In meta-analyses totaling 6,540 cases and 2,096,759 controls, we identified 10 associations with HCC, of which five (in KLF15, HSD17B13, APOE, HFE, and MTARC1) have not previously been implicated in HCC at genome-wide statistical significance. Known associations in PNPLA3, TM6SF2, TERT, IFNL4, and HLA-DP1 were confirmed. All associations except KLF15 were validated in independent cohorts totaling 7,630 cases and 733,689 controls. The largest per-allele effect was seen for TM6SF2 (beta = 0.61) followed by PNPLA3 (0.55), HFE (0.45), IFNL4 (0.31), APOE (0.27), HSD17B13, HLA-DP1, and TERT (all 0.21), and MTARC1 (0.17). The identified variants had comparable effects on incident HCC in individuals with prevalent obesity, a high alcohol intake, diabetes, or cirrhosis. Mendelian randomization analyses confirmed the causal role of obesity in HCC. We found strong correlations between genetic effects on HCC and hepatic steatosis (r2 = 0.75), and HCC and cirrhosis (r2 = 0.69), whereas only three loci (APOE, HFE, and TERT) had concordant effects on HCC and biliary tract cancer. Conclusions:We identified and validated nine genetic variants associated with an increased risk of HCC development. Impact and implications:The genetic underpinnings of HCC remain largely unknown. In this genome-wide association meta-analysis totaling 6,540 cases with HCC and 2.1 million controls, we identified and validated nine genetic loci to associate with the risk of HCC. A deeper insight into genetic factors that affect the risk of HCC could improve our ability to predict and ultimately prevent or treat this deadly cancer.

Dysregulation of genes encoding the homologous to E6AP C-terminus (HECT) E3 ubiquitin ligases has been linked to cancer and structural birth defects. One member of this family, the HECT-domain-containing protein 1 (HECTD1), mediates developmental pathways, including cell signaling, gene expression, and embryogenesis. Through GeneMatcher, we identified 14 unrelated individuals with 15 different variants in HECTD1 (10 missense, 3 frameshift, 1 nonsense, and 1 splicing variant) with neurodevelopmental disorders (NDDs), including autism, attention-deficit/hyperactivity disorder, and epilepsy. Of these 15 HECTD1 variants, 10 occurred de novo, 3 had unknown inheritance, and 2 were compound heterozygous. While all individuals in this cohort displayed NDDs, no genotype-phenotype correlation was apparent. Conditional knockout of Hectd1 in the neural lineage in mice resulted in microcephaly, severe hippocampal malformations, and complete agenesis of the corpus callosum, supporting a role for Hectd1 in embryonic brain development. Functional studies of select variants in C. elegans revealed dominant effects, including either change-of-function or loss-of-function/haploinsufficient mechanisms, which may explain phenotypic heterogeneity. Significant enrichment of de novo variants in HECTD1 was also shown in an independent cohort of 53,305 published trios with NDDs or congenital heart disease. Thus, our clinical and functional data support a critical requirement of HECTD1 for human brain development.