BACKGROUND:Chromatinopathies represent a genetically and clinically heterogeneous group of neurodevelopmental disorders (NDDs) caused by pathogenic variants in genes regulating chromatin structure and function. The phenotypic overlap and genetic complexity of these conditions pose significant diagnostic challenges, often resulting in unresolved variants of uncertain significance (VUS). RESULTS:We investigated a cohort of 400 routine diagnostic individuals with NDD using whole-exome sequencing and genome-wide DNA methylation profiling via the clinically validated EpiSign assay. Episignature classification was used to aid in variant interpretation and to define molecular subtypes of chromatinopathy. Seventeen percent of individuals (67/400) harbored variants in chromatinopathy-associated genes, including 55 novel variants. DNA methylation profiling was performed in 60 individuals with 62 variants in chromatin regulator genes. Of these, 26 individuals (43%) exhibited disorder-specific episignatures consistent with the associated clinical diagnosis. Importantly, methylation profiles supported the pathogenicity of several variants previously classified as VUS and demonstrated diagnostic concordance with known disease-associated genes including ANKRD11, SETD5, KMT2A, KDM5C, CHD8, and others. CONCLUSION:Our study highlights the improved diagnostic yield and clinical utility of combining genomic and epigenomic profiling in patients with clinically and/or genetically suspected chromatinopathies. Integration of EpiSign analysis facilitated variant reclassification, delineated genotype-epigenotype-phenotype correlations, and expanded the episignature atlas for rare neurodevelopmental disorders.

BACKGROUND: Hearing loss (HL) is one of the most common congenital conditions and exhibits substantial clinical and genetic heterogeneity. More than 150 genes are associated with non-syndromic hearing loss (NSHL), while over 600 genes are linked to syndromic hearing loss (SHL). Importantly, the absence of additional clinical symptoms at the time of diagnosis does not necessarily exclude SHL. An increasing number of functionally disruptive variants in a growing number of genes have been shown to initially present as isolated HL, only later revealing syndromic features. METHODS: We analyzed clinical data from 111 patients across 102 unrelated families, selected from over 600 individuals negative for GJB2 and STRC variants. Molecular inversion probe panel, exome, or genome sequencing was performed, and patients were retrospectively divided into three subgroups following variant interpretation. Molecular docking was performed on select non-synonymous substitutions. RESULTS: Subgroup 1 included 30 patients with variants in neurodevelopmental disorder (NDD)-associated genes. HL was the first clinical manifestation in 80% of patients, with it being the sole first symptom in half. Subgroup 2 was comprised of 52 patients with variants in SHL-associated genes unrelated to NDD, while subgroup 3 included 29 patients with variants in genes associated with both NSHL and SHL, such as SLC26A4 and USH1C. In subgroups 2 and 3, HL was the sole initial symptom for nearly all patients (92% and 100%, respectively). Across the cohort, 99 variants in 44 genes were identified, including 36 novel variants. CONCLUSION: The frequent absence of syndromic features at presentation may lead to genetic testing or analysis restricted to NSHL-associated genes. Our findings highlight the critical role of comprehensive genomic testing in the diagnostic workup of HL, enabling earlier identification of syndromic forms and facilitating timely medical management, genetic counseling, and anticipatory care.

Structural variants (SVs) of the nebulin gene (NEB), including intragenic duplications, deletions, and copy number variation of the triplicate region, are an established cause of recessively inherited nemaline myopathies and related neuromuscular disorders. Large deletions have been shown to cause dominantly inherited distal myopathies. Here we provide an overview of 35 families with muscle disorders caused by such SVs in NEB. Using custom Comparative Genomic Hybridization arrays, exome sequencing, short-read genome sequencing, custom Droplet Digital PCR, or Sanger sequencing, we identified pathogenic SVs in 35 families with NEB-related myopathies. In 23 families, recessive intragenic deletions and duplications or pathogenic gains of the triplicate region segregating with the disease in compound heterozygous form, together with a small variant in trans, were identified. In two families the SV was, however, homozygous. Eight of these families have not been described previously. In 12 families with a distal myopathy phenotype (of which 10 are previously unpublished), eight unique, large deletions encompassing 52–97 exons in either heterozygous (n = 10) or mosaic (n = 2) state were identified. In the families where inheritance was recessive, no correlation could be made between the types of variants and the severity of the disease. In contrast, all patients with large dominant deletions in NEB had milder, predominantly distal muscle weakness. For the first time, we establish a clear and statistically significant association between large NEB deletions and a form of distal myopathy. In addition, we provide the hitherto largest overview of the spectrum of SVs in NEB.

Pre-mRNA splicing is a fundamental step in protein synthesis within a cell. Malfunctions during this process can lead to dysfunctional proteins and thus, to a variety of different human diseases. Mis-splicing can be caused by genetic variants influencing many different molecular processes, e.g. splice donor and splice acceptor site variants. Today, the consequences of these variants can be calculated via different in-silico programs. Due to the complexity of the splicing process, however, these predictions are not always correct and should not be used as stand-alone criteria for the classification of potentially disease-causing variants. Therefore, in case RNA from an appropriate tissue is not available additional in-vitro studies, such as a minigene splice assay, which allows functional analyses of potentially disease-causing variants, are necessary to demonstrate an effect on splicing. One example of a human developmental disorder occasionally caused by mis-splicing of transcripts is craniosynostosis. This congenital disorder is defined by the premature fusion of one or multiple cranial sutures in the neurocranium. To date, numerous mutation types in more than 50 genes which are involved in a broad range of different cellular functions and pathways have been associated with craniosynostosis. For instance, the TCF12 gene encoding the bHLH (basic helix-loop-helix) protein TCF12 (transcription factor 12) is linked to Craniosynostosis 3 (OMIM: 615314) which exhibits a Saethre-Chotzen (OMIM:101400) like phenotype. In this study, we report a pipeline for functional validation of potential splice site altering variants. First, we describe the identification of two novel genetic variants and revalidation of one previously described genetic variant in patients with craniosynostosis. According to in-silico predictions, the splicing of the corresponding transcripts is altered, and the variants are potentially disease causing. We subsequently classify the consequences of alterations in TCF12 experimentally. The suspected aberrant splicing was investigated via an in-vitro minigene splice assay. In two out of three variants, the in-silico prediction and in-vitro experiments were consistent. In all variants a significantly reduced transcriptional activity was demonstrated. In summary, the combination of in-silico prediction and functional assays allowed us to classify the variants as likely pathogenic without the need for additional patient material.

Microtubule-actin cross-linking factor 1 (MACF1) is a large protein of the spectraplakin family, which is essential for brain development. MACF1 interacts with microtubules through the growth arrest-specific 2 (Gas2)-related (GAR) domain. Heterozygous MACF1 missense variants affecting the zinc-binding residues in this domain result in a distinctive cortical and brain stem malformation. Evidence for other MACF1-associated disorders is still limited. Here, we present a cohort of 45 individuals with heterozygous or bi-allelic MACF1 variants to explore the phenotypic spectrum and assess possible pathogenic relevance. We observe that de novo heterozygous missense variants in the EF-hand domains also result in distinctive brain malformation and provide experimental evidence that variants in the EF-hand/GAR module increase microtubule binding, suggestive of a toxic gain of function. Notably, no phenotype-genotype correlation was possible for the remaining heterozygous variants in other domains. A clinical review of eight families with bi-allelic variants reveals a possible complex neurodevelopmental syndrome of the central and peripheral nervous systems. In these individuals, bi-allelic variants mostly affect the Plakin domain. Furthermore, RNA sequencing and chromatin immunoprecipitation (ChIP) analyses of human fetal brain tissue reveal five MACF1 isoforms with region-specific expression, differing in their exon 1 transcription start sites but splicing to a common exon 2. This differential expression explains the frontal-predominant lissencephaly in an individual with a homozygous stop-gain in exon 1 (MACF1-204: c.70C>T [p.Arg24∗]), as this isoform is preferentially expressed in the frontal cortex. We conclude that MACF1-related disorders are strictly linked to domain function and the level of transcript expression, explaining the observed wide clinical heterogeneity.

Dear Editors, Sporadic basal cell carcinoma (BCC) is caused by aberrations in the hedgehog (Hh) signaling pathway. Within this pathway, SUFU acts as a tumor suppressor. PTCH1 is mutated in 70% whereas SUFU is mutated in about 8% of BCCs.1 SUFU loss of heterozygosity (LOH) only leads to BCC, when additional mutations in tumor suppressor genes such as p53 or oncogenes such as PTCH1 are present.2 Although the majority of BCCs arises sporadically, genodermatoses such as basal cell nevus syndrome (BCNS), which is mostly caused by a mutation in PTCH1 and SMO, can also lead to BCC formation.3 Requena et al. first described an autosomal dominant genodermatosis characterized by various infundibulocystic BCCs, a rare and more indolent subtype, and was therefore termed multiple hereditary infundibluocystic BCC syndrome (MHIBCC).4 Schulman et al. later associated MHIBCC with a proposed germline SUFU mutation that was found in five tumor samples and in normal mucosal tissue of the patient.5 These previously described MHIBCC cases showed multiple well-differentiated, indolent, and mostly infundibulocystic basal cell carcinomas on the face and genitals, but no other characteristics of basal cell nevus syndrome. We report on a 65-year-old woman with more than 40 histologically confirmed BCCs (Figure 1). Family history was negative for BCC and medulloblastoma. Our patient reported no prior brain abnormalities (shown in a recent MRI), no further comorbidities, no signs of immunosuppression, no occupational risk factors, no prior cancers (including no prior therapy with ionizing irradiation) and no signs of other cancer prone syndromes. Additionally, no sun sensitivity was reported. However, occasional sunbathing and use of tanning beds in early adulthood were reported. The majority (> 30) of tumors were found on her face but BCCs formed at atypical sites, including her left palm (Figure 2c), groin (Figure 2b), and the outer edge of the left foot (Figure 2d) as well. Clinical examination also showed multiple skin-colored papules on the face (Figure 2a), which developed in her adult life and had been histologically diagnosed as sebaceous hyperplasia. Germline mutation screening was performed by targeted next generation sequencing with a four gene panel including the full coding sequence of PTCH1, BAP1, FLCN and SUFU (NM_016169.3). Samples were sequenced with an Illumina MiSeq (Illumina, San Diego, CA, USA). A heterozygous nonsense mutation in exon 4 was detected in the SUFU gene (c.595C>T), which led to a stop signal on codon 199 (p.Gln199Stop). This nonsense mutation is located on the N-terminal domain of the protein and might cause a nonsense-mediated mRNA decay or at least results in a truncated protein. The variant has not yet been described, but loss of function mutations in the tumor suppressor gene SUFU are known to cause BCNS. This is of particular importance for the usage of Hh-inhibitors in patients with advanced or metastatic BCC. While SUFU mutations confer resistance to such treatment, tumors with an additional or sole aberration in PTCH1 are likely sensitive to Hh-inhibitors.6 Genetic analysis of three BCCs and two sebaceous hyperplasias using a commercial NGS panel (targeted panel sequencing using the Oncomine Comprehensive Assay v3, ThermoFisher) was performed. Libraries were sequenced on the Ion GeneStudio S5 Plus platform and analyzed with Torrent Suite and Ion Reporter Software (ThermoFisher) (Supplementary Table S1). Neither sebaceous hyperplasia showed any likely pathogenic or pathogenic mutations. However, the BCC on the foot yielded PTCH1 (likely pathogenic) and TP53 (pathogenic) missense mutations while two BCCs on the face showed no relevant aberration in PTCH1 or other genes analyzed. Interestingly, two BCCs (foot, face) showed missense mutations in both the oncogene KNSTRN and the tumor suppressor gene ATRX. Three of four point mutations affecting the ATRX and KNSTRN gene were not characterized biologically and were therefore categorized as variant of unknown significance (VUS).7 The p.Ser24Phe mutation in KNSTRN was described as likely pathogenic/likely loss of function according to OncoKB. A detailed overview of all pathogenic/likely pathogenic variants and VUS is shown in Supplementary Table S1. We present a patient with MHIBCC harboring a nonsense germline mutation in SUFU. So far, no truncating SUFU variants associated with MHIBCC have been described. Germline mutations in SUFU have mostly been associated with pediatric medulloblastoma,8 while they are rarely found in patients with BCNS.9 Both KNSTRN and ATRX encode for proteins involved in chromosomal regulation. Chromosome dysfunction due to mutations in KNSTRN and ATRX likely causes chromosomal instability and promotes oncogenesis. The oncogene KNSTRN has previously been associated with early stage (<2 cm in size) BCC.10 Tumor suppressor ATRX has been described in the context of glioma development,11 which is, like BCC, associated with SUFU mutations. The yet unclear interactions between SUFU and ATRX might help understand the concurrent evolution of both glioma and BCC in BCNS patients. We conclude that the patient's germline mutation in SUFU led to the formation of multiple infundibulocystic BCCs. Our data indicate that the emergence of BCCs in MIHBB at atypical sites such as groin, palm, and foot might be associated with additional mutations in oncogenes and/or tumor suppressors. Open access funding enabled and organized by Projekt DEAL. None.

Sehr geehrte Herausgeber, das Basalzellkarzinom (BCC) wird durch Mutationen im Hedgehog (Hh)-Signalweg verursacht. Innerhalb dieses Signalwegs fungiert SUFU als Tumorsuppressor. PTCH1 ist bei 70 % der BCC mutiert, während SUFU bei etwa 8 % der BCC mutiert ist.1 Ein Verlust der Heterozygotie (LOH) von SUFU führt nur dann zur Entstehung eines BCC, wenn zusätzliche Mutationen in Tumorsuppressorgenen wie p53 oder Onkogenen wie PTCH1 vorliegen.2 Obwohl die Mehrheit der BCC sporadisch auftritt, können Genodermatosen wie das Basalzellnävus-Syndrom (BCNS), das hauptsächlich durch eine Mutation in PTCH1 und SMO verursacht wird, auch zur Bildung von BCC führen.3 Requena et al. beschrieben erstmals eine autosomal-dominante Genodermatose, die durch verschiedene infundibulozystische BCC, eine seltene und weniger aggressive Unterart, charakterisiert ist, und wurde daher als multiples hereditäres infundibulozystisches BCC-Syndrom (MHIBCC) bezeichnet.4 Schulman et al. brachten MHIBCC später mit einer Keimbahnmutation in SUFU in Verbindung, die in fünf Tumorproben und im normalen Schleimhautgewebe des Patienten gefunden wurde.5 Diese MHIBCC-Fälle zeigten multiple gut differenzierte, indolente und hauptsächlich infundibulozystische Basalzellkarzinome im Gesicht und an den Genitalien, aber keine anderen Merkmale des BCNS. Wir berichten über eine 65-jährige Frau mit über 40 histologisch bestätigten BCC (Abbildung 1). Die Familienanamnese war negativ für BCC und Medulloblastom. Unsere Patientin berichtete von keinen früheren Hirnanomalien (bestätigt durch eine durchgeführte MRT-Untersuchung), keiner beruflichen Risikoexposition, keine weiteren Begleiterkrankungen, keine Anzeichen von Immunsuppression, keine früheren Krebserkrankungen (einschließlich keiner vorherigen Behandlung mit ionisierender Bestrahlung) und keine Anzeichen anderer familiären Krebssyndrome. Außerdem wurde keine Sonnenempfindlichkeit berichtet. Gelegentliches Sonnenbaden und die Nutzung von Sonnenbänken wurden allerdings in jungen Erwachsenenjahren berichtet. Die Mehrheit (> 30) der Tumoren wurde im Gesicht gefunden, aber BCC traten auch an untypischen Stellen auf, einschließlich der linken Handfläche (Abbildung 2c), der Leistengegend (Abbildung 2b) und des äußeren Randes des linken Fußes (Abbildung 2d). Die klinische Untersuchung zeigte auch mehrere hautfarbene Papeln im Gesicht (Abbildung 2a), die sich im Erwachsenenalter entwickelt hatten und histologisch als Talgdrüsenhyperplasien diagnostiziert wurden. Eine Keimbahnmutationsanalyse wurde durch gezielte Next-Generation-Sequenzierung (NGS) mit einem Vier-Gen-Panel durchgeführt, das die vollständige Kodierungssequenz von PTCH1, BAP1, FLCN und SUFU (NM_016169.3) umfasste. Die Proben wurden mit einem Illumina MiSeq (Illumina, San Diego, CA, USA) sequenziert. Es wurde eine heterozygote Nonsense-Mutation im Exon 4 des SUFU-Gens (c.595C>T) nachgewiesen, die zu einem Stopp-Signal im Codon 199 führte (p.Gln199Stop). Diese Nonsense-Mutation befindet sich in der N-terminalen Domäne des Proteins und könnte zu einem Nonsense-vermittelten mRNA-Abbau führen oder zumindest zu einem (…) trunkierten Protein (…) Protein führen. Die Variante wurde noch nicht beschrieben, aber Loss-of-Function-Mutationen im Tumorsuppressorgen SUFU verursachen das BCNS. Dies ist besonders wichtig für den Einsatz von Hh-Inhibitoren bei Patienten mit fortgeschrittenem oder metastasiertem BCC. Während SUFU-Mutationen zu einer Resistenz führen, sind Tumoren mit zusätzlichen Abweichungen in PTCH1 wahrscheinlich empfindlich gegenüber Hh-Inhibitoren.6 Die genetische Analyse von drei BCC und zwei Talgdrüsenhyperplasien wurde mit einem kommerziellen NGS-Panel (gezielte Panel-Sequenzierung mit dem Oncomine Comprehensive Assay v3, ThermoFisher) durchgeführt. Die Bibliotheken wurden auf der Ion GeneStudio S5 Plus-Plattform sequenziert und mit Torrent Suite und Ion Reporter Software (ThermoFisher) analysiert (Tabelle S1, Online-Supplement). Beide Talgdrüsenhyperplasien zeigten keine wahrscheinlich pathogenen (likely pathogenic) oder pathogenen (pathogenic) Mutationen. Das BCC am Fuß zeigte PTCH1 (likely pathogenic) und TP53 (pathogenic) Missense-Mutationen, während zwei BCC im Gesicht keine relevanten Mutationen in PTCH1 oder anderen analysierten Genen zeigten. Interessanterweise zeigten zwei BCC (Fuß, Gesicht) Missense-Mutationen sowohl im Onkogen KNSTRN als auch im Tumorsuppressorgen ATRX. Drei von vier Punktmutationen, die die Gene ATRX und KNSTRN betreffen, wurden biologisch bisher nicht charakterisiert und daher als Variante unbekannter Bedeutung (VUS) kategorisiert.7 Die p.Ser24Phe-Mutation in KNSTRN wurde gemäß OncoKB als likely pathogenic/likely loss of function beschrieben. Eine detaillierte Übersicht über alle pathogenic/likely pathogenic Varianten und VUS ist in der Tabelle S1 (Online-Supplement) dargestellt. Zusammenfassend beschreiben wir eine Patientin mit MHIBCC, die eine Nonsense-Keimbahnmutation in SUFU aufweist. Bisher wurden noch keine trunkierende SUFU-Varianten im Zusammenhang mit MHIBCC beschrieben. Keimbahnmutationen in SUFU wurden bisher hauptsächlich mit kindlichem Medulloblastom8 in Verbindung gebracht und nur selten bei Patienten mit BCNS9 gefunden. Sowohl KNSTRN als auch ATRX kodieren für Proteine, die an der Regulation von Chromosomen beteiligt sind. Chromosomale Dysfunktion aufgrund von Mutationen in KNSTRN und ATRX führt wahrscheinlich zu chromosomaler Instabilität und fördert die Onkogenese. Das Onkogen KNSTRN wurde zuvor mit BCC im Frühstadium (< 2 cm Größe) assoziiert.10 Das Tumorsuppressorgen ATRX wurde im Zusammenhang mit der Entwicklung von Gliomen,11 beschrieben, die wie BCC mit SUFU-Mutationen assoziiert sind. Die noch unklaren Wechselwirkungen zwischen SUFU und ATRX könnten helfen, die gleichzeitige Entwicklung von Gliomen und BCC bei BCNS-Patienten zu verstehen. Wir schlussfolgern, dass die Keimbahnmutation der Patientin in SUFU zur Bildung von mehreren infundibulozystischen BCC geführt hat. Unsere Daten deuten darauf hin, dass das Auftreten von BCC bei MHIBCC an untypischen Stellen wie Leiste, Handfläche und Fuß mit zusätzlichen Mutationen in Onkogenen und/oder Tumorsuppressorgenen assoziiert sein könnte. Open access Veröffentlichung ermöglicht und organisiert durch Projekt DEAL. Keiner.

AnamneseDer 31-jährige Patient stellte sich mit seit 3 Monaten bestehender, subakut aufgetretener Visusminderung des

Background Mucopolysaccharidosis type III (Sanfilippo syndrome) is a lysosomal storage disorder, caused by a deficiency in the heparan-N-sulfatase enzyme involved in the catabolism of the glycosaminoglycan heparan sulfate. It is characterized by early nonspecific neuropsychiatric symptoms, followed by progressive neurocognitive impairment in combination with only mild somatic features. In this patient group with a broad clinical spectrum a significant genotype-phenotype correlation with some mutations leading to a slower progressive, attenuated course has been demonstrated. Case presentation Our patient had complications in the neonatal period and was diagnosed with Mucopolysaccharidosis IIIa only at the age of 28 years. He was compound heterozygous for the variants p.R245H and p.S298P, the latter having been shown to lead to a significantly milder phenotype. Conclusions The diagnostic delay is even more prolonged in this patient population with comorbidities and a slowly progressive course of the disease.

Background The chromosomal region 11p15.5 harbours two imprinting centres (H19/IGF2:IG-DMR/IC1, KCNQ1OT1:TSS-DMR/IC2). Molecular alterations of the IC2 are associated with Beckwith-Wiedemann syndrome (BWS), whereas only single patients with growth retardation and Silver-Russell syndrome (SRS) features have been reported. CNVs in 11p15.5 account for less than 1% of patients with BWS and SRS, and they mainly consist of duplications of both ICs either affecting the maternal (SRS) or the paternal (BWS) allele. However, this correlation does not apply to smaller CNVs, which are associated with diverse clinical outcomes. Methods and results We identified a family with a 132 bp deletion within the KCNQ1OT1 gene, associated with growth retardation in case of paternal transmission but a normal phenotype when maternally inherited. Comparison of molecular and clinical data with cases from the literature helped to delineate its functional relevance. Conclusion Microdeletions within the paternal IC2 affecting the KCNQ1OT1 gene have been described in only five families, and they all include the differentially methylated region KCNQ1OT1:TSS-DMR/IC2 and parts of the KCNQ1 gene. However, these deletions have different impacts on the expression of both genes and the cell-cycle inhibitor CDKN1C. They thereby cause different phenotypes. The 132 bp deletion is the smallest deletion in the IC2 reported so far. It does not affect the IC2 methylation in general and the coding sequence of the KCNQ1 gene. Thus, the deletion is only associated with a growth retardation phenotype when paternally transmitted but not with other clinical features in case of maternal inheritance as observed for larger deletions.

The La-related protein 7 (LARP7) forms a complex with the nuclear 7SK RNA to regulate RNA polymerase II transcription. It has been implicated in cancer and the Alazami syndrome, a severe developmental disorder. Here, we report a so far unknown role of this protein in RNA modification. We show that LARP7 physically connects the spliceosomal U6 small nuclear RNA (snRNA) with a distinct subset of box C/D small nucleolar RNAs (snoRNAs) guiding U6 2'-O-methylation. Consistently, these modifications are severely compromised in the absence of LARP7. Although general splicing remains largely unaffected, transcriptome-wide analysis revealed perturbations in alternative splicing in LARP7-depleted cells. Importantly, we identified defects in 2'-O-methylation of the U6 snRNA in Alazami syndrome siblings carrying a LARP7 mutation. Our data identify LARP7 as a bridging factor for snoRNA-guided modification of the U6 snRNA and suggest that alterations in splicing fidelity contribute to the etiology of the Alazami syndrome.

Inherited cardiomyopathies are characterized by clinical and genetic heterogeneity that challenge genetic diagnostics. In this study, we examined the diagnostic benefit of exome data compared to targeted gene panel analyses, and we propose new candidate genes. We performed exome sequencing in a cohort of 61 consecutive patients with a diagnosis of cardiomyopathy or primary arrhythmia, and we analyzed the data following a stepwise approach. Overall, in 64% of patients, a variant of interest (VOI) was detected. The detection rate in the main sub-cohort consisting of patients with dilated cardiomyopathy (DCM) was much higher than previously reported (25/36; 69%). The majority of VOIs were found in disease-specific panels, while a further analysis of an extended panel and exome data led to an additional diagnostic yield of 13% and 5%, respectively. Exome data analysis also detected variants in candidate genes whose functional profile suggested a probable pathogenetic role, the strongest candidate being a truncating variant in STK38. In conclusion, although the diagnostic yield of gene panels is acceptable for routine diagnostics, the genetic heterogeneity of cardiomyopathies and the presence of still-unknown causes favor exome sequencing, which enables the detection of interesting phenotype–genotype correlations, as well as the identification of novel candidate genes.

The clinical impact of duplications affecting the 11p15.5 region is difficult to predict, and depends on the parent-of-origin of the affected allele as well as on the type (deletion, duplication), the extent and genomic content of the variant. Three unrelated families with inheritance of duplications affecting the IC1 region in 11p15.5 through two generations but different phenotypes (Beckwith-Wiedemann and Silver-Russell syndromes, normal phenotype) are reported. The inconsistent phenotypic patterns of carriers of the same variant strongly indicate the impact of cis- and/or trans-acting modifiers on the clinical outcome of IC1 duplication carriers.

Height is a heritable and highly heterogeneous trait. Short stature affects 3% of the population and in most cases is genetic in origin. After excluding known causes, 67% of affected individuals remain without diagnosis. To identify novel candidate genes for short stature, we performed exome sequencing in 254 unrelated families with short stature of unknown cause and identified variants in 63 candidate genes in 92 (36%) independent families. Based on systematic characterization of variants and functional analysis including expression in chondrocytes, we classified 13 genes as strong candidates. Whereas variants in at least two families were detected for all 13 candidates, two genes had variants in 6 (UBR4) and 8 (LAMA5) families, respectively. To facilitate their characterization, we established a clustered network of 1025 known growth and short stature genes, which yielded 29 significantly enriched clusters, including skeletal system development, appendage development, metabolic processes, and ciliopathy. Eleven of the candidate genes mapped to 21 of these clusters, including CPZ, EDEM3, FBRS, IFT81, KCND1, PLXNA3, RASA3, SLC7A8, UBR4, USP45, and ZFHX3. Fifty additional growth-related candidates we identified await confirmation in other affected families. Our study identifies Mendelian forms of growth retardation as an important component of idiopathic short stature.