Unexpected role of SIX1 variants in craniosynostosis: expanding the phenotype of SIX1-related disorders

BackgroundPathogenic heterozygous SIX1 variants (predominantly missense) occur in branchio-otic syndrome (BOS), but an association with craniosynostosis has not been reported.MethodsWe investigated probands with craniosynostosis of unknown cause using whole exome/genome (n=628) or RNA (n=386) sequencing, and performed targeted resequencing of SIX1 in 615 additional patients. Expression of SIX1 protein in embryonic cranial sutures was examined in the Six1nLacZ/+ reporter mouse.ResultsFrom 1629 unrelated cases with craniosynostosis we identified seven different SIX1 variants (three missense, including two de novo mutations, and four nonsense, one of which was also present in an affected twin). Compared with population data, enrichment of SIX1 loss-of-function variants was highly significant (p=0.00003). All individuals with craniosynostosis had sagittal suture fusion; additionally four had bilambdoid synostosis. Associated BOS features were often attenuated; some carrier relatives appeared non-penetrant. SIX1 is expressed in a layer basal to the calvaria, likely corresponding to the dura mater, and in the mid-sagittal mesenchyme.ConclusionCraniosynostosis is associated with heterozygous SIX1 variants, with possible enrichment of loss-of-function variants compared with classical BOS. We recommend screening of SIX1 in craniosynostosis, particularly when sagittal±lambdoid synostosis and/or any BOS phenotypes are present. These findings highlight the role of SIX1 in cranial suture homeostasis.

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A de novo paradigm for male infertility

10.1101/2021.02.27.433155 ◽

2021 ◽

Author(s):

MS Oud ◽

RM Smits ◽

HE Smith ◽

FK Mastrorosa ◽

GS Holt ◽

...

Keyword(s):

Male Infertility ◽

De Novo ◽

P Value ◽

Missense Mutations ◽

Loss Of Function ◽

De Novo Mutations ◽

Systematic Analysis ◽

Significant Enrichment

IntroductionDe novo mutations (DNMs) are known to play a prominent role in sporadic disorders with reduced fitness1. We hypothesize that DNMs play an important role in male infertility and explain a significant fraction of the genetic causes of this understudied disorder. To test this hypothesis, we performed trio-based exome-sequencing in a unique cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare protein altering DNMs were classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of Loss-of-Function (LoF) DNMs in LoF-intolerant genes (p-value=1.00×10-5) as well as predicted pathogenic missense DNMs in missense-intolerant genes (p-value=5.01×10-4). One DNM gene identified, RBM5, is an essential regulator of male germ cell pre-mRNA splicing2. In a follow-up study, 5 rare pathogenic missense mutations affecting this gene were observed in a cohort of 2,279 infertile patients, with no such mutations found in a cohort of 5,784 fertile men (p-value=0.009). Our results provide the first evidence for the role of DNMs in severe male infertility and point to many new candidate genes affecting fertility.

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A Novel Frameshift Mutation in KAT6A Is Associated with Pancraniosynostosis

Journal of Pediatric Genetics ◽

10.1055/s-0040-1710330 ◽

2020 ◽

Author(s):

Fady P. Marji ◽

Jennifer A. Hall ◽

Erin Anstadt ◽

Suneeta Madan-Khetarpal ◽

Jesse A. Goldstein ◽

...

Keyword(s):

Intellectual Disability ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Frameshift Mutation ◽

De Novo ◽

Cranial Sutures ◽

Speech Delay ◽

First Case ◽

Whole Exome ◽

Suture Fusion

AbstractDe novo heterozygous mutations in the KAT6A gene give rise to a distinct intellectual disability syndrome, with features including speech delay, cardiac anomalies, craniofacial dysmorphisms, and craniosynostosis. Here, we reported a 16-year-old girl with a novel pathogenic variant of the KAT6A gene. She is the first case to possess pancraniosynostosis, a rare suture fusion pattern, affecting all her major cranial sutures. The diagnosis of KAT6A syndrome is established via recognition of its inherent phenotypic features and the utilization of whole exome sequencing. Thorough craniofacial evaluation is imperative, craniosynostosis may require operative intervention, the delay of which may be detrimental.

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A de novo paradigm for male infertility

10.21203/rs.3.rs-332732/v1 ◽

2021 ◽

Author(s):

Joris Veltman ◽

Manon Oud ◽

Roos Smits ◽

Hannah Smith ◽

Francesco Mastrorosa ◽

...

Keyword(s):

Male Infertility ◽

De Novo ◽

P Value ◽

Missense Mutations ◽

Loss Of Function ◽

De Novo Mutations ◽

Systematic Analysis ◽

Significant Enrichment

Abstract De novo mutations (DNMs) are known to play a prominent role in many sporadic disorders with reduced fitness. We hypothesize that DNMs play an important role in male infertility and explain a significant fraction of the genetic causes of this understudied disorder. We performed a trio-based exome-sequencing study in a unique cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare protein altering DNMs were classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of Loss-of-Function (LoF) DNMs in LoF-intolerant genes (p-value=1.00x10-5) as well as predicted pathogenic missense DNMs in missense-intolerant genes (p-value=5.01x10-4). One DNM gene identified, RBM5, is an essential regulator of male germ cell pre-mRNA splicing. In a follow-up study, 5 rare pathogenic missense mutations affecting this gene were observed in a cohort of 2,279 infertile patients, with no such mutations found in a cohort of 5,784 fertile men (p-value=0.009). Our results provide the first evidence for the role of DNMs in severe male infertility and point to many new candidate genes affecting fertility.

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A de novo paradigm for male infertility

Nature Communications ◽

10.1038/s41467-021-27132-8 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

M. S. Oud ◽

R. M. Smits ◽

H. E. Smith ◽

F. K. Mastrorosa ◽

G. S. Holt ◽

...

Keyword(s):

Male Infertility ◽

De Novo ◽

Missense Mutations ◽

Loss Of Function ◽

De Novo Mutations ◽

Systematic Analysis ◽

Significant Enrichment ◽

Infertile Patients

AbstractDe novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF < 0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes (p-value = 1.00 × 10−5) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes (p-value = 5.01 × 10−4) in contrast to predicted benign de novo mutations. One gene we identify, RBM5, is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men (p-value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility.

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De novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1709255114 ◽

2017 ◽

Vol 114 (35) ◽

pp. E7341-E7347 ◽

Cited By ~ 29

Author(s):

Andrew T. Timberlake ◽

Charuta G. Furey ◽

Jungmin Choi ◽

Carol Nelson-Williams ◽

Erin Loring ◽

...

Keyword(s):

De Novo ◽

Erk Signaling ◽

Loss Of Function ◽

De Novo Mutations ◽

Neurodevelopmental Outcomes ◽

Locus Heterogeneity ◽

Syndromic Craniosynostosis ◽

New Genes ◽

Morphogenetic Protein ◽

Nuclear Targets

Non-syndromic craniosynostosis (NSC) is a frequent congenital malformation in which one or more cranial sutures fuse prematurely. Mutations causing rare syndromic craniosynostoses in humans and engineered mouse models commonly increase signaling of the Wnt, bone morphogenetic protein (BMP), or Ras/ERK pathways, converging on shared nuclear targets that promote bone formation. In contrast, the genetics of NSC is largely unexplored. More than 95% of NSC is sporadic, suggesting a role for de novo mutations. Exome sequencing of 291 parent–offspring trios with midline NSC revealed 15 probands with heterozygous damaging de novo mutations in 12 negative regulators of Wnt, BMP, and Ras/ERK signaling (10.9-fold enrichment, P = 2.4 × 10−11). SMAD6 had 4 de novo and 14 transmitted mutations; no other gene had more than 1. Four familial NSC kindreds had mutations in genes previously implicated in syndromic disease. Collectively, these mutations contribute to 10% of probands. Mutations are predominantly loss-of-function, implicating haploinsufficiency as a frequent mechanism. A common risk variant near BMP2 increased the penetrance of SMAD6 mutations and was overtransmitted to patients with de novo mutations in other genes in these pathways, supporting a frequent two-locus pathogenesis. These findings implicate new genes in NSC and demonstrate related pathophysiology of common non-syndromic and rare syndromic craniosynostoses. These findings have implications for diagnosis, risk of recurrence, and risk of adverse neurodevelopmental outcomes. Finally, the use of pathways identified in rare syndromic disease to find genes accounting for non-syndromic cases may prove broadly relevant to understanding other congenital disorders featuring high locus heterogeneity.

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A de novo variant in CASK gene causing intellectual disability and brain hypoplasia: A Case Report and Literature Review

10.21203/rs.3.rs-317232/v1 ◽

2021 ◽

Author(s):

Ying Zhang ◽

Yanyan Nie ◽

Yu Mu ◽

Jie Zheng ◽

Xiaowei Xu ◽

...

Keyword(s):

Intellectual Disability ◽

Mental Disorders ◽

De Novo ◽

Clinical Symptoms ◽

Clinical Manifestations ◽

De Novo Mutation ◽

Loss Of Function ◽

Bioinformatics Analyses ◽

Whole Exome ◽

De Novo Variant

Abstract Background：The pathogenic variation of CASK gene can cause CASK related mental disorders. The main clinical manifestations are microcephaly with pontine and cerebellar hypoplasia, X-linked mental disorders with or without nystagmus and FG syndrome. The main pathogenic mechanism is the loss of function of related protein caused by mutation. We reported a Chinese male newborn with a de novo variant in CASK gene. Case presentation：We present an 18-day-old baby with intellectual disability and brain hypoplasia. Whole-exome sequencing was performed, which detected a hemizygous missense mutation c.764G>A of CASK gene. The mutation changed the 255th amino acid from Arg to His. Software based bioinformatics analyses were conducted to infer its functional effect.Conclusions：In this paper, a de novo mutation of CASK gene was reported. Moreover, a detailed description of all the cases described in the literature is reported.CASK mutations cause a variety of clinical phenotypes. Its diagnosis is difficult due to the lack of typical clinical symptoms. Genetic testing should be performed as early as possible if this disease is suspected. This case provides an important reference for the diagnosis and treatment of future cases.

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Identification of a β-Arrestin 2 Mutation Related to Autism by Whole-Exome Sequencing

BioMed Research International ◽

10.1155/2020/8872577 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9

Author(s):

Yunfei Tang ◽

Yamei Liu ◽

Lei Tong ◽

Shini Feng ◽

Dongshu Du ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Developmental Stages ◽

De Novo ◽

Repetitive Behavior ◽

Brain Regions ◽

Autism Spectrum ◽

Potential Contribution ◽

De Novo Mutations ◽

Whole Exome

Autism spectrum disorder (ASD) is a complex neurological disease characterized by impaired social communication and interaction skills, rigid behavior, decreased interest, and repetitive activities. The disease has a high degree of genetic heterogeneity, and the genetic cause of ASD in many autistic individuals is currently unclear. In this study, we report a patient with ASD whose clinical features included social interaction disorder, communication disorder, and repetitive behavior. We examined the patient’s genetic variation using whole-exome sequencing technology and found new de novo mutations. After analysis and evaluation, ARRB2 was identified as a candidate gene. To study the potential contribution of the ARRB2 gene to the human brain development and function, we first evaluated the expression profile of this gene in different brain regions and developmental stages. Then, we used weighted gene coexpression network analysis to analyze the associations between ARRB2 and ASD risk genes. Additionally, the spatial conformation and stability of the ARRB2 wild type and mutant proteins were examined by simulations. Then, we further established a mouse model of ASD. The results showed abnormal ARRB2 expression in the mouse ASD model. Our study showed that ARRB2 may be a risk gene for ASD, but the contribution of de novo ARRB2 mutations to ASD is unclear. This information will provide references for the etiology of ASD and aid in the mechanism-based drug development and treatment.

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Primary aldosteronism associated with a germline variant in CACNA1H

BMJ Case Reports ◽

10.1136/bcr-2018-229031 ◽

2019 ◽

Vol 12 (5) ◽

pp. e229031 ◽

Cited By ~ 1

Author(s):

Kendra Wulczyn ◽

Edward Perez-Reyes ◽

Robert L Nussbaum ◽

Meyeon Park

Keyword(s):

Primary Aldosteronism ◽

De Novo ◽

Missense Variant ◽

Laboratory Evaluation ◽

Loss Of Function ◽

Aldosterone Secretion ◽

Whole Exome ◽

Voltage Dependent ◽

Cell Current ◽

Voltage Sensing Domain

The CACNA1H gene encodes the pore-forming α1 subunit of the T-type voltage-dependent calcium channel CaV3.2, expressed abundantly in the adrenal cortex. Mutations in CACNA1H are associated with various forms of primary aldosteronism (PA), including familial hyperaldosteronism type 4 (FH4). We describe a patient with refractory hypokalaemia and elevated aldosterone secretion independent of renin activity. Despite the absence of overt hypertension in this patient, the laboratory evaluation was consistent with a diagnosis of PA. Whole-exome sequencing revealed a de novo missense variant, R890H, in the voltage sensing domain of CACNA1H. Expression of the variant channel in cells resulted in decreased whole-cell current, consistent with a loss-of-function. We hypothesise this variant is the genetic cause of pathological aldosterone secretion in this patient, and thereby expand the current understanding of the genetic basis of FH4.

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Molecular Dissection of Neurodevelopmental Disorder-Causing Mutations in CYFIP2

Cells ◽

10.3390/cells9061355 ◽

2020 ◽

Vol 9 (6) ◽

pp. 1355

Author(s):

Matthias Schaks ◽

Michael Reinke ◽

Walter Witke ◽

Klemens Rottner

Keyword(s):

De Novo ◽

Neurodevelopmental Disorder ◽

Small Gtpases ◽

Normal Brain ◽

Loss Of Function ◽

De Novo Mutations ◽

Neuronal Morphogenesis ◽

Variable Extent ◽

Regulatory Complex ◽

Almost All

Actin remodeling is frequently regulated by antagonistic activities driving protrusion and contraction downstream of Rac and Rho small GTPases, respectively. WAVE regulatory complex (WRC), which primarily operates downstream of Rac, plays pivotal roles in neuronal morphogenesis. Recently, two independent studies described de novo mutations in the CYFIP2 subunit of WRC, which caused intellectual disability (ID) in humans. Although mutations had been proposed to effect WRC activation, no experimental evidence for this was provided. Here, we made use of CRISPR/Cas9-engineered B16-F1 cell lines that were reconstituted with ID-causing CYFIP variants in different experimental contexts. Almost all CYFIP2-derived mutations (7 out of 8) promoted WRC activation, but to variable extent and with at least two independent mechanisms. The majority of mutations occurs in a conserved WAVE-binding region, required for WRC transinhibition. One mutation is positioned closely adjacent to the Rac-binding A site and appears to ease Rac-mediated WRC activation. As opposed to these gain-of-function mutations, a truncating mutant represented a loss-of-function variant and failed to interact with WRC components. Collectively, our data show that explored CYFIP2 mutations frequently, but not always, coincide with WRC activation and suggest that normal brain development requires a delicate and precisely tuned balance of neuronal WRC activity.

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Molecular signaling in pathogenesis of craniosynostosis: the role of fibroblast growth factor and transforming growth factor–β

Neurosurgical FOCUS ◽

10.3171/2011.5.focus1197 ◽

2011 ◽

Vol 31 (2) ◽

pp. E7 ◽

Cited By ~ 8

Author(s):

Harvey Chim ◽

Sunil Manjila ◽

Alan R. Cohen ◽

Arun K. Gosain

Keyword(s):

Growth Factor ◽

Fibroblast Growth Factor ◽

Transforming Growth Factor ◽

Transforming Growth Factor Β ◽

Cranial Sutures ◽

Fibroblast Growth ◽

Molecular Signaling ◽

Ongoing Research ◽

Suture Fusion

The interplay of signals between dura mater, suture mesenchyme, and brain is essential in determining the fate of cranial sutures and the pathogenesis of premature suture fusion leading to craniosynostosis. At the forefront of research into suture fusion is the role of fibroblast growth factor and transforming growth factor–β, which have been found to be critical in the cell-signaling cascade involved in aberrant suture fusion. In this review, the authors discuss recent and ongoing research into the role of fibroblast growth factor and transforming growth factor–β in the etiopathogenesis of craniosynostosis.

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