A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder.

SNIP1 (Smad nuclear interacting protein 1) is a widely expressed transcriptional suppressor of the TGF-β signal-transduction pathway which plays a key role in human spliceosome function. Here, we describe extensive genetic studies and clinical findings of a complex inherited neurodevelopmental disorder in 35 individuals associated with a SNIP1 NM_024700.4:c.1097A>G, p.(Glu366Gly) variant, present at high frequency in the Amish community. The cardinal clinical features of the condition include hypotonia, global developmental delay, intellectual disability, seizures, and a characteristic craniofacial appearance. Our gene transcript studies in affected individuals define altered gene expression profiles of a number of molecules with well-defined neurodevelopmental and neuropathological roles, potentially explaining clinical outcomes. Together these data confirm this SNIP1 gene variant as a cause of an autosomal recessive complex neurodevelopmental disorder and provide important insight into the molecular roles of SNIP1, which likely explain the cardinal clinical outcomes in affected individuals, defining potential therapeutic avenues for future research.

Introduction

Smad proteins entail a family of structurally-related intracellular proteins that act as transcriptional regulators of the transforming growth factor-beta (TGF-β)/bone morphogenetic protein (BMP) pathway, crucially important for a variety of cellular processes including cell growth, differentiation and apoptosis [1]. Three categories of Smad are recognised: receptor-regulated (R-Smads) and common mediator (Co-Smads), which form trimeric functional units of two R-Smads with the common Co-Smad partner SMAD4 and inhibitory/anti (I-Smads), acting together to inhibit these functional units [2].

The Smad nuclear interacting protein 1 (SNIP1) gene encodes a widely expressed nuclear transcriptional regulator of several important molecular signalling pathways involved in embryogenesis. This evolutionarily conserved protein is made up of 396 amino acids, comprising a two-part nuclear localisation signal (NLS) and a forkhead-associated (FHA) domain (Fig 1H) [3,4]. The N-terminus NLS interacts with several Smads in the TGF-β signalling pathway [3], and inhibits the p65/RELA subunit of nuclear factor kappa-beta (NFkB; a primary transcription factor in proinflammatory signalling pathways) to act as a transcriptional repressor [4]. The SNIP1 N-terminal domain also acts to inhibit transcription via competitive binding of transcriptional co-activators CREBBP (CREB-binding protein) and EP300 (E1A-binding protein, 300 kDa) [3,4]. The C-terminal FHA domain of SNIP1 has been shown to enhance transcriptional activity via direct binding to the oncoprotein c-MYC (a key regulator of cell proliferation and growth-promoting pathways) [5]. Further molecular pathways that may be regulated by SNIP1 activity include those involved in carcinogenesis, including regulation of cyclin D1 expression [6] and ATR checkpoint kinase-dependent pathways [7], as well as heat shock elements through regulation of heat shock factor-mediated transcription of heat shock proteins [8]. SNIP1 also forms a component of the human activated spliceosome [9], as part of the retention and splicing (RES) complex, which plays a crucial role in splicing and retention of pre-mRNA [10]. Genetic variants leading to disruption of the TGF-β/BMP molecular signalling pathway have been implicated in the pathogenesis of a number of inherited disorders, in particular connective tissue disorders associated with craniofacial (e.g. cleft palate and craniosynostosis), cardiovascular (e.g. aortic aneurysm and syndromic aortopathies), and musculoskeletal (e.g. disorders of endochondral ossification, bone growth, remodelling and limb development) outcomes [11].

Fig 1

Homozygous Clinical features of individuals affected by SNIP1-related disorder. (A-C) Clinical features of three affected infants comprising of (A) craniosynostosis, proptosis, (A-C) downslanting palpebral fissures, microretrognathia, cupids bow upper lip and small upturned bulbous nose (B) hypotonia, tracheostomy, and gastrostomy feeding tube (C) metopic ridge, asymmetrical skull shape. (D) Photograph of older child, additional phenotypic features illustrated include; micrognathia, wide-mouth and dental crowding. (E) Simplified pedigree of 12 interlinking Amish nuclear families illustrating 22 individuals (of 35 investigated, which could be linked into a single pedigree using available Amish ancestry databases) affected with SNIP1-related disorder and confirmed to be homozygous for the SNIP1 NM_024700.3: c.1097A>G, p.(Glu366Gly) variant. (F) Sequence chromatogram of the c.1097A>G, p.(Glu366Gly) variant (red arrow). (G) Multi-species alignment showing conservation of the polypeptide region encompassing the p.(Glu366Gly) alteration (red arrow). (H) Schematic diagram of the SNIP1 protein identifying the N-terminus nuclear localisation signal (NLS) domain (yellow box), C-terminus forkhead-associated (FHA) domain (orange box) and location of the c.1097A>G, p.(Glu366Gly) variant (red box). (I) Visualisation of differential expression results showing genes grouped by log(fold change) (x-axis) and log(adjusted p-value) (y-axis). Dashed vertical lines show the log(fold change) cut-off used to identify differentially expressed genes showing the largest relative expression changes (green points). The dashed horizontal line shows the log(adjusted p-value) cut-off used to identify significantly differentially expressed genes (blue points). Genes that are both significantly differentially expressed and show the largest change in expression are coloured red. Non-significant genes with low changes in expression are shown in grey. A selection of differentially expressed genes are labelled.

The Amish are descended from a relatively small group of Swiss-German individuals that emigrated from Europe to the USA in two main waves of migration in the 18th and 19th centuries. Puffenberger et al (2012) previously described three Old Order Amish individuals with symptomatic epilepsy and skull dysplasia and identified a homozygous NM_024700.4:c.1097A>G, p.(Glu366Gly) variant in SNIP1 as the likely cause of the condition (autosomal recessive psychomotor retardation, epilepsy, and craniofacial dysmorphism; PMRED, MIM #614501) [12]. These three individuals displayed neonatal hypotonia, severe global developmental delay, dysmorphic features, a “lumpy” skull surface, poor feeding, intractable seizures, brain abnormalities on MRI, and other congenital defects. Here we present comprehensive genetic, clinical and gene transcript functional outcomes stemming from the investigation of 35 Amish individuals with an autosomal recessive neurodevelopmental disorder, corroborating this SNIP1 gene variant as a cause of this disease.

Results

Clinical features

35 of 51 identified individuals from 21 interrelated Old Order Amish families (19 males; 16 females, aged 1 month to 26 years) with molecularly confirmed SNIP1-related disorder were evaluated (see Fig 1, and Table 1 for clinical summary, includes new findings for two affected individuals previously published by Puffenberger et al 2012 [12]). Six children died between ages 9 months and 11 years as a consequence of infection, sudden cardiopulmonary arrest, or accidental drowning. Substantial phenotypic variation was observed between affected individuals, including within sibships.

Table 1

Clinical features of 35 individuals with SNIP1-related disorder.

	Mean age in years (range)	6.9 (0.2–26)
Neurological phenotype		(% affected)
	Global developmental delay (severe, non-verbal)	100%
	Hypotonia	100%
	Hyporeflexia	100%
	Seizures	100%
	Abnormal brain MRI (ventriculomegaly, white matter defects)	50%
	Behavioural problems (irritability, autistic features, ADHD)	75%
Cardiopulmonary features
	Upper airway abnormalities (laryngomalacia, apnoea, stridor)	75%
	Congenital heart defects (ASD, VSD, aortic coarctation)	60%
	Cardiomyopathy	12%
Visual and hearing phenotype
	Horizontal nystagmus and/or strabismus	45%
	Failed newborn hearing screen (conductive loss)	21%
Gastroenterological features
	Feeding difficulties	100%
	Small for gestational age	54%
	Pulmonary aspiration with/without gastrostomy tube	46%
Endocrine phenotype
	Hypothyroidism	25%
	Hypoglycaemia	21%
Dysmorphic features
	Abnormal skull shape (irregular surface, craniosynostosis)	100%
	High arched palate	100%
	Wide mouth with cupids bow upper lip	100%
	Micrognathia with/without Pierre Robin sequence	30%
	Short hands with tapered fingers	54%
	Spinal abnormalities (scoliosis, sacral dimple, tethered cord)	21%
	Hernias (umbilical, inguinal)	21%
	Congenital talipes equinovarus	13%

Abbreviations: MRI; magnetic resonance imaging, ADHD; attention deficit hyperactivity disorder, ASD; atrial septal defect, VSD; ventricular septal defect.

The cardinal clinical features of SNIP1-related disorder include: hypotonia, global developmental delay, intellectual disability, seizures, a characteristic facial appearance and skull abnormalities. Craniofacial features (Fig 1A–1D) include midface hypoplasia, a wide mouth with downturned corners and thin cupids bow upper lip, large tongue, high arched palate, microretrognathia (Pierre Robin sequence with or without cleft palate in three patients), malocclusion, small upturned bulbous nose, long palpebral fissures and proptosis (in individuals with craniosynostosis). Other dysmorphic features include brachydactyly, broad thumbs, single palmar crease, congenital talipes equinovarus, pes planus, toenail hypoplasia and pectus excavatum (Table 1). Skull morphological abnormalities were observed and ranged from normocephaly to severe multi-suture craniosynostosis with Cloverleaf appearance of the skull in five individuals, and included an irregular skull surface with variable calvarium thickness and bony dysplasia (Fig 1A–1D).

The neurological spectrum of the syndrome is variable and includes seizures, hypotonia with hypo/areflexia and pervasive behavioural abnormalities. Seizures are a cardinal feature of the disorder with all affected individuals developing epilepsy. Seizure types include focal and generalised intractable seizures (myoclonic, absence, tonic-clonic) of infantile or childhood onset. EEG was abnormal in all individuals assessed, with no characteristic pattern, findings included diffuse background slowing and frequent focal or multifocal discharges (see S1 Text for detailed serial EEG findings observed in eight affected individuals). In some infants, seizures initially presented as apnea or breath-holding spells and subclinical seizures were detected in six individuals. Seizures can be triggered or exacerbated by febrile illness, sleep deprivation and hypoglycemic episodes. There were no antiepileptic medications identified that consistently provide effective seizure control (defined as manageable frequency of seizures) and several individuals display multiple drug resistant epilepsy. Some individuals suffered severe developmental regression following status epilepticus, with two reported to have subsequent permanent hemiparesis. Individuals identified in late childhood/adolescence are often diagnosed with a mixed tone spastic quadriplegic cerebral palsy, likely reflecting hypoxic injury after long-term untreated/unrecognised seizures. Irritability and sleep/wake dysregulation are seen in infancy and early childhood. Behavioural diagnoses include autism spectrum disorder and attention deficit disorder. Most affected individuals achieved independent ambulation (age range 3–10 years), and some communicate with signs, gestures and sounds. Neuroimaging was available for 18 individuals, all confirmed to have abnormalities, including hydrocephalus, ventriculomegaly, white matter abnormalities, thin corpus callosum, hypomyelination, irregular cortical ribbon, Chiari malformation, absence of the septum pellucidum, hypoplastic optic nerves and septo-optic dysplasia [12]. Cerebral arteriovenous malformation (AVM) was reported in a single individual. Other clinical features associated with SNIP1-related disorder include a variable spectrum of congenital cardiac defects (60% of individuals), including hypoplastic left heart syndrome, aortic stenosis and bicuspid aortic valve, aortic coarctation, aortic root dilatation, atrial septal defect (ASD), ventricular septal defect (VSD), patent ductus arteriosus (PDA), pulmonary artery stenosis and mitral valve regurgitation, 12% of affected individuals developed cardiomyopathy (left ventricular noncompaction). Affected individuals commonly displayed upper airway respiratory difficulties in the neonatal period, including laryngomalacia, pharyngomalacia and subglottic stenosis of variable severity, causing a weak cry, stridor and apnea, occasionally requiring tracheostomy and supplementary home oxygen.

Spinal abnormalities were seen in 23% including sacral dimple, tethered cord and scoliosis in older children. Other features include pectus excavatum and hypoplastic ribs in a single individual. Poor feeding in the neonatal period is universal and many require a gastrostomy tube to both aid nutrition and reduce risk of aspiration pneumonia. Gastrointestinal features reported include gastroesophageal reflux, paraoesophageal hernia (type III), intestinal malrotation, hepatomegaly and umbilical and inguinal hernias. Intrauterine growth retardation (IUGR) and failure to thrive was also common. Endocrine abnormalities including hypoglycemia, hypothyroidism, hypothermia and dyshormonogenesis were identified in a small proportion of patients. Ophthalmic features include strabismus, horizontal nystagmus and myopia. Auditory features include chronic otitis media and hearing loss, with 20% failing newborn hearing screening.

Genetic studies

Our initial studies involved the investigation of four affected individuals (X:30, X:31, XI:6 and XI:7) from two nuclear families, on whom samples were originally available (Fig 1E). In order to map the likely chromosomal location of the causative gene a genome-wide screen was undertaken to identify putative autozygous genomic regions, assuming homozygosity for the same ancestral founder variant, which entails the most common cause of recessive monogenic disorders in the Amish. Inspection of resultant genotypes identified a single region of homozygosity greater than 1Mb common to all four affected individuals, a small (1.65Mb) genomic region on chromosome 1p34.3 delimited by SNP markers rs6667450 and rs10889902 (NC_000001.11:g.36,492,230–38,143,653; S1 Fig), highly likely to contain the disease locus, comprising 17 genes. To identify candidate genetic variants in this region WES data on two individuals (X:16 and X:42) identified only a single potentially pathogenic sequence variant (Chr1:g.37537842T>C; RefSeq NM_024700.4:c.1097A>G, p.(Glu366Gly) [hg38]) in exon four of the SNIP1 gene, located in the chromosome 1p34.3 critical interval, previously identified by Puffenberger et al 2012 [12]. Dideoxy sequencing validated the presence of the variant (Fig 1F), which cosegregated as appropriate for an autosomal recessive condition. Subsequent targeted genetic investigation of additional affected individuals that were identified, confirmed homozygosity of the SNIP1 variant in 35 individuals, with all parents being heterozygous for the variant and all unaffected siblings being heterozygous for the variant or wild type (Fig 1E). Multiple species alignment confirms this amino acid is highly conserved across species orthologs (Fig 1G) and is located close to the FHA domain at the SNIP1 C-terminus (Fig 1H). Inspection of our in-house Amish control database (>5000 individuals) determined that the SNIP1 NM_024700.4:c.1097A>G, p.(Glu366Gly) variant is present at an allele frequency of between 0.5% (Pennsylvania Amish) and 1.4% (Ohio/Indiana/Wisconsin Amish) in this founder population, with no unaffected individuals being homozygous for this variant. The variant is present in gnomAD (v3.1) with an allele frequency of 0.001% with 11 heterozygotes (10 Amish) and no homozygous individuals listed, with multiple in silico tools predicting the variant to be pathogenic. The SNIP1 variant was assessed according to ACMG variant classification criteria as ‘pathogenic’ (see S2 Text).

Effect of SNIP1 variant on gene expression and cellular pathways

In order to provide improved insight into SNIP1 gene function, and outcomes of the NM_024700.4:c.1097A>G; p.(Glu366Gly) gene variant on gene expression, we performed whole transcriptome sequencing on six affected individuals from four distinct nuclear sibships, alongside sex-matched controls. We performed a power estimation using the characteristics of our RNA-Seq data that included sequencing depth, dispersion and log fold change to estimate the probability of finding differentially expressed genes in our data. This power calculation indicated a >50% probability (power = 0.59) of finding significantly differentially expressed genes given our sample size and data characteristics, confirming that the number of samples and quality of the RNA-Seq data are sufficient to identify differentially expressed genes.

Differentially expressed genes with a false discovery rate (FDR) adjusted p-value of <0.05 identified a list of 75 significantly upregulated genes, and 109 significantly downregulated genes (Tables A and B in S1 Table). A log fold change of >1.5 was used as an additional cut off for both up and downregulated genes to select only those that show the largest relative changes in expression (Fig 1I). These genes were assessed for known clinical associations and involvement in conditions with overlap with the clinical features in affected individuals enrolled on this study (Tables A and B in S2 Table). Additionally Reactome pathway analysis [13] combining both up and downregulated genes identified a total of 30 significantly overrepresented pathways (entities p value <0.05) (Tables A-C in S3 Table); the most overrepresented pathway was the TGF-β receptor signalling in epithelial to mesenchyme pathway with differential expression of three genes (upregulation of PARD3 and downregulation of F11R and RPS27A) (Table 2). Tissue expression of genes up/downregulated in individuals with SNIP1-related disorder was assessed using GTex, Broad Institute 2021 (S2 and S3 Figs), which identified that several of the upregulated genes are highly expressed within the brain, although this was not apparent for downregulated genes.

Table 2

List of the 10 most differentially expressed (both up/downregulated) gene pathways.

Pathway name	Pathway identifier	#Entities found	#Entities total	Entities ratio	Entities pValue	Entities FDR	Genes
TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)	R-HSA-2173791	3	19	0.00129	0.002827	0.43317	PARD3 ; RPS27A; F11R
Transcriptional regulation of pluripotent stem cells	R-HSA-452723	4	45	0.00306	0.004461	0.43317	NR5A1; EPAS1; ATP9A
RUNX1 regulates transcription of genes involved in BCR signaling	R-HSA-8939245	2	7	0.00048	0.004820	0.43317	BLK
CDC6 association with the ORC:origin complex	R-HSA-68689	2	11	0.00075	0.011458	0.43317	E2F2; E2F3
Signaling by NOTCH3	R-HSA-9012852	4	63	0.00428	0.014027	0.43317	PLEKHG1 ; PLXND1; RPS27A
Pexophagy	R-HSA-9664873	2	13	0.00088	0.015702	0.43317	EPAS1 ; RPS27A
NOTCH3 Intracellular Domain Regulates Transcription	R-HSA-9013508	3	36	0.00245	0.016072	0.43317	PLEKHG1 ; PLXND1
Erythrocytes take up oxygen and release carbon dioxide	R-HSA-1247673	2	16	0.00109	0.023123	0.43317	SLC4A1; HBD
Oncogene Induced Senescence	R-HSA-2559585	3	42	0.00285	0.023970	0.43317	E2F2; E2F3; RPS27A
Defective binding of RB1 mutants to E2F1,(E2F2, E2F3)	R-HSA-9661069	2	17	0.00115	0.025859	0.43317	E2F2; E2F3

List of the top 10 human gene pathways that are most differentially expressed (both up/downregulated) from Reactome [13] overrepresentation analysis of significantly up/downregulated genes in six affected individuals compared with sex-matched controls and a log(fold change) >1.5 were used in gene set enrichment analysis of pathway and gene ontology. Pathways with an entities P value of <0.05 were considered significantly overrepresented. Genes in bold were upregulated, those in normal font were downregulated. FDR, false discovery rate is the probability corrected for multiple comparisons.

Discussion

Here, we describe our studies of a complex syndromic autosomal recessive neurodevelopmental disorder due to a biallelic SNIP1 variant (NM_024700.4:c.1097A>G, p.(Glu366Gly)), which we found to be common amongst the Old Order Amish. A total of fifty-one Old Order Amish individuals were identified with SNIP1-related disorder, among 27 sibships. Seventy-six percent (n = 39) are currently living (age range 6 months to 30 years), while 24% (n = 12) are deceased (age of death between 1 week and 11 years). Forty-nine individuals were confirmed to be homozygous for the SNIP1 variant, two individuals were not genotyped, but displayed characteristic clinical features of the disorder and had an affected sibling confirmed to be homozygous for the SNIP1 founder variant. In total thirty-five individuals with SNIP1-related disorder were comprehensively clinically evaluated and included in this study.

The condition involves a recognizable neurodevelopmental phenotype comprising of a characteristic craniofacial appearance, skull abnormalities, developmental delay, intellectual disability and variable additional congenital malformations, neurological, cardiovascular, respiratory and gastrointestinal features. Seizures, starting in infancy, are a universal feature and can include any combination of focal or generalised, myoclonic, absence or tonic-clonic forms. Our findings determine that clinical management strategies should be targeted at preventing life-threatening complications and optimising psychomotor development and are summarized in Table 3.

Table 3

SNIP1-related disorder clinical advice and guidelines.

Medical care:	Children should be under the care of a general or community paediatrician to monitor their general health and development.Clinical management strategies should be targeted at preventing life-threatening complications and optimising psychomotor development.
Seizures:	Children should be under the care of specialist neurology services for careful optimisation of anticonvulsant medications to treat apnea in infancy, maintain seizure control, and prevent status epilepticus and consequent developmental regression.Early EEG should be carried out in infants with suspected apneic episodes.Neuroimaging should be performed at diagnosis.
Congenital heart disease:	Echocardiogram should be performed at diagnosis to screen for congenital heart defects
Gastrointestinal:	We recommend elective gastrostomy tube placement to support growth and limit pulmonary aspiration.An upper gastrointestinal study and renal ultrasound should be considered to screen for congenital anomalies.
Speech and language:	Speech and language therapy should be commenced at an early stage to maximise neurocognitive outcome.
Motor development:	Physical and occupational therapies should be commenced at an early stage to maximise neurocognitive outcome.
Vision/Hearing:	Yearly ophthalmology and audiology assessments are recommended.
Endocrine:	Infants and children should be monitored for hypoglycaemia and hypothyroidism as these are easily treatable.
Behavioural abnormalities:	Behavioural therapy (including Applied Behaviour Analysis) is beneficial in older affected children who have autism spectrum disorder.
Sleep:	Many children experience sleep dysregulation. Melatonin has been used successfully in some children.
Education:	An assessment of special educational needs should be carried out so that an individualized educational plan can be put in place at school.Some children have behavioural difficulties requiring additional support and one-to-one instruction.

These guidelines are based on the most commonly identified features in individuals with SNIP1-related disorder. There is a wide range in variability of the clinical presentation and individual patients should have a personalized plan to reflect their own clinical features.

We recommend elective gastrostomy tube placement to support growth and limit pulmonary aspiration, as well as careful optimisation of anticonvulsant medications to treat apnea in infancy, maintain seizure control, and prevent status epilepticus and consequent developmental regression. These simple interventions can reduce hospitalizations, alleviate suffering, and prolong life. Supportive therapies (occupational, speech, and physical therapy) should be commenced at an early stage to maximise neurocognitive outcome for patients with SNIP1-related disorder. Behavioural therapy (including Applied Behaviour Analysis) is beneficial in older affected children who have autism spectrum disorder. We advise that an EEG should be obtained at an early stage in infants with SNIP1-related disorder and suspected apneic episodes. Neuroimaging should be performed at diagnosis, and echocardiogram should be undertaken to screen for congenital heart defects. An upper gastrointestinal study, head ultrasound, and renal ultrasound should also be considered to screen for other congenital anomalies. Individuals should also be monitored for hypoglycemia and hypothyroidism as these are easily treatable. Yearly ophthalmology and audiology assessments are recommended.

While the pathomolecular outcomes associated with the SNIP1 NM_024700.4:c.1097A>G, p.(Glu366Gly) substitution remain unclear, SNIP1 null mouse models display embryonic lethality indicating that this Amish variant may be unlikely to result in complete loss of function [14]. While no other biallelic variants in SNIP1 have conclusively been associated with genetic disease to date, Jacher and Innis (2018) reported a 17-year-old female with a de novo 2.3 Mb interstitial deletion at 1q34.3q34.2 that encompassed 43 genes, of which only two (SNIP1 and RSPO1) were potentially linked with genetic disease genes at the time of publication [15]. This female had global developmental delay, mild intellectual disability, congenital defects, vocal cord paralysis, delayed bone age, and skeletal deformities. The authors concluded that haploinsufficiency of SNIP1 was the most likely cause of the female’s neurodevelopmental phenotype, although they were not able to confirm this nor rule out contributions of the other genes involved. In addition to NM_024700.4:c.1097A>G, p.(Glu366Gly), ClinVar lists six further “pathogenic” entries for SNIP1: five entries as part of a multiple gene deletion, and one SNIP1 missense variant (NM_024700.4:c.331C>T; p.(Arg111Cys)) in an individual with Rolandic epilepsy, with low allele frequency (0.00018) and no homozygotes in gnomAD v2.1/v3.1. Previous studies and online gene expression databases (GTEx: https://gtexportal.org/home/) show that SNIP1 mRNA expression is ubiquitous, consistent with the diverse multisystem phenotypical outcomes associated with variation in SNIP1, with particularly high expression in neurological, cardiac and skeletal systems [3,8]. SNIP1 has been identified as a regulator of several transcription factors, including Smads (transcription factors in the TGF-β pathway), NF-kB (a transcription factor in proinflammatory and immune signalling pathways) and c-MYC (a transcription factor in cell proliferation and growth-promoting pathways) as well as binding co-activators for transcription, including CREBBP and EP300 [3-5]. The p.(Glu366Gly) SNIP1 amino acid substitution is located in close proximity to the forkhead association (FHA) domain and within the C-terminal 30 amino acids, entailing a ‘low complexity or intrinsically disordered region’ (IDR). Thus while this region lacks a well-defined 3D structure for modelling analyses, it is strongly conserved across multiple species (Fig 1G) and is highly likely to represent a functionally important region of SNIP1 [16].

In TGF-β/BMP pathway signalling, ligand binding to the TGF-β receptor results in phosphorylation of Smad 2/3 which bind to Smad4, resulting in nuclear translocation of the Smad complex and recruitment of co-activators EP300 and CREBBP to induce the expression of target genes. The SNIP1 C-terminus interacts with Smads 1/2, while the N-terminus NLS binds both Smad4 and CREBBP/EP300 coactivators; overexpression of SNIP1 inhibits CREBBP/EP300 and the formation of Smad4 complexes, thereby suppressing transcription and inhibiting multiple gene responses to TGF-β signalling [3]. Disorders involving Smads and other components of the TGF-β pathway include connective tissue, craniofacial and skeletal disorders, several of which display overlapping clinical features with SNIP1-related disorder detailed here. This includes systemic aortopathies, including for example Loeys-Dietz syndrome (LDS), characterized by congenital cardiac defects including bicuspid aortic valve, septal defects, patent ductus arteriosus, mitral valve regurgitation, aortic root dilatation, in addition to craniosynostosis, cleft palate, hypertelorism, micrognathia, talipes, and scoliosis [17]. Additionally, other conditions associated with disruption of the TGF-β pathway include the brachdactyly syndromes (e.g. type A2, B2 and C), which display the overlapping clinical feature of brachydactyly. SNIP1 has also been implicated in the inhibition of transcription factor NF-kB by competitive binding with the RelA subunit for binding to the coactivator EP300. The NF-kB family of transcription factors are regulators of a large number of genes involved in immune and inflammatory processes, cell growth and development. NF-kB is composed of dimeric complexes of five different subunits, RelA, RelB, RelC, NF-kB1 and NF-kB2, which mediate gene transcription by binding kB enhancer with the coactivator EP300 [18]. Disruption of NF-kB in several animal models results in severe developmental defects during embryogenesis including dorsal-ventral patterning, limb, liver, skin, lung, neural, notochord, muscle, skeletal, and hematopoietic defects (reviewed in Espín-Palazón et al 2016) [19], again mirroring some outcomes identified in SNIP1-related disorder. Additionally other studies identified SNIP1 downregulation in individuals with dilated cardiomyopathic hearts, and in aortic banding-induced mice hearts [20], shown to be mediated by NF-kB signalling. Remarkably, SNIP1 inhibition of this pathway reduced cardiac hypertrophy, while blocking the NF-kB pathway reduced the adverse effects of SNIP1 deficiency; these findings are notable as left ventricular noncompaction is also a feature seen in SNIP1-related disorder.

Zhang et al confirmed that SNIP1 forms a component of the human activated spliceosome (Bact complex) [9], as part of the retention and splicing (RES) complex with Bud13 and RBMX2 [21], which plays a crucial role in splicing and retention of pre-mRNA [10]. Disruption of spliceosome components have been associated with several neurodevelopmental disorders involving craniofacial defects, for example Guion-Almeida type mandibulofacial dysostosis, Nager syndrome, and cerebrocostomandibular syndrome, which also display several overlapping features with SNIP1-related disorder including midface hypoplasia, cleft palate, developmental delay, intellectual disability, congenital cardiac defects and scoliosis [22]. This identifies a further possible mechanism of disease pathogenesis in SNIP1-related disorder. To gain insight into the aberrant molecular processes which may derive from the NM_024700.4:c.1097A>G, p.(Glu366Gly) SNIP1 variant and underlie this condition, we undertook whole transcriptome studies of individuals with SNIP1-related disorder. These studies were inherently limited due to the modest number of samples available for study and through the obvious limitations of comparing gene transcriptions profiles in blood, with tissues in which clinical outcomes are primarily manifested (brain). However such studies are warranted in genes such as SNIP1 with ubiquitous tissue expression profiles, where blood studies may provide important insight into the key molecular signalling pathways likely influenced by genetic variation. Notably of the 11 upregulated and 32 downregulated gene expression profiles with an associated clinical phenotype which were most notably altered, 24 had a previously established association with neurological disease. This includes five genes (ROBO1, SOX5, CNTNAP2, PAFAH1B1 and TSNARE1) associated with seizures, the cardinal feature of SNIP1-related disorder. Of these ROBO1 (roundabout guidance receptor 1), the gene identified to be most upregulated in affected individuals with SNIP1-related disorder, is a member of the neural cell adhesion molecule (NCAM) family involved in axonal migration. Notably biallelic sequence variants within ROBO1 are associated with a neurodevelopmental disorder displaying many of the cardinal features seen in SNIP1-related disorder including neurodevelopmental delay, white matter abnormalities [23], epilepsy, autistic features [24], VSD and tetralogy of Fallot [25]. The expression of CNTNAP2 encoding contactin-associated protein 2 (CASPR2), a member of the neurexin superfamily involved in neuron-glia interactions [26], was also notably increased by SNIP1 gene variation. Disruption of CNTNAP2 is associated with autosomal recessive Pitt-Hopkins-like syndrome (also known as cortical dysplasia focal epilepsy syndrome; MIM 610042) characterized by neurodevelopmental delay, hypotonia, hyporeflexia, seizures of multiple types, neuronal migration abnormalities, autistic features, and attention deficits [27,28]. One further gene expression profile strongly upregulated includes SYT1 (synaptotagmin 1), an integral membrane protein of synaptic vesicles which binds calcium to trigger neurotransmitter release at the synapse [29]. Variation within the SYT1 gene has previously been associated with an autosomal dominant neurodevelopmental disorder (Baker-Gordon syndrome; OMIM 618218) characterized by neurodevelopmental delay, hypotonia, autistic features, non-specific white matter abnormalities, feeding problems, dysmorphic features, scoliosis, strabismus, nystagmus and self-injurious behaviour [30,31]. Further to these, the other 40 gene expression profiles most influenced by variation in SNIP1 includes two other genes (PAFAH1B1 and TOR1AIP1) associated with brain structural abnormalities, five (PLXND1, TNS1, CAVIN4, EYA4 and TOR1AIP1) associated with cardiac defects including several conotruncal heart defects and cardiomyopathy, and two (LINGO2 and SOX5) with dysmorphic craniofacial features (Tables A and B in S2 Table) overlapping features of SNIP1-related disorder. Further we investigated whether any up or down regulated genes were known interactors in SNIP1-regulated pathways, defining two downregulated genes (BMPR1A and ACVR1C) involved in the TGF-β pathway, two dysregulated genes (BLNK and IL8, up and downregulated respectively) which are components of the NF-kB pathway, and one upregulated gene (BCL-7A) within the c-MYC pathway [32]. Reactome analysis identified that the most highly dysregulated pathway was the TGF-β receptor signalling in epithelial to mesenchymal transition pathway, further supporting the critical role of SNIP1 within this pathway. Given this, it seems likely that the NM_024700.4:c.1097A>G, p.(Glu366Gly) SNIP1 substitution likely results in the clinical outcomes seen through the disrupted regulation of multiple molecular roles and signalling pathways important for human development, potentially defining candidate therapeutic targets for future research for SNIP1-related disorder. Taken together, these findings consolidate biallelic variants within the SNIP1 gene as a cause of a complex neurodevelopmental disorder and provide important insight into the biological role and key molecular processes perturbed by pathogenic variation of SNIP1.

Materials and methods

Ethics statement

This study was carried out in accordance with institutional ethics review board-approved research protocols from the University of Arizona (10-0050-10) and Akron Children’s Hospital (IRB 986876–3). All individuals (or their families) whose data is included in this study provided written informed consent and where applicable specific written consent for publication of photographs.

Clinical and genetic studies

We identified a total of 51 individuals of Old Order Amish descent affected with SNIP1-related disorder through clinics who provide care for the Amish communities (The Community Health Clinic; Indiana, New Leaf Center; Ohio, Center for Special Children; Wisconsin, Clinic for Special Children; Pennsylvania). We conducted a historical review of clinical information and undertook physical examination and a parent survey for 35 of the affected children available for evaluation considering geographical restrictions. Blood/buccal samples were obtained for DNA extraction using standard techniques from affected individuals, their parents and unaffected siblings with informed consent. Single-nucleotide polymorphism (SNP) genotyping was performed using HumanCytoSNP-12 (v2.1 beadchip array, Illumina). WES (BGI Seq) involved: Agilent Sureselect Whole Exome v6 targeting, read alignment (BWA-MEM (v0.7.17), mate-pairs fixed and duplicates removed (Picard v2.15.0), InDel realignment/base quality recalibration (GATK v3.7.0), single-nucleotide variant (SNV)/InDel detection (GATK HaplotypeCaller), annotation (Alamut v1.10) and read depth (GATK DepthOfCoverage). Copy number variants (CNVs) were detected using both ExomeDepth (https://cran.r-project.org/web/packages/ExomeDepth) and SavvyCNV [33]. Dideoxy sequencing was undertaken using standard techniques.

Transcript analyses

Analysis was carried out for six affected individuals (3 male, 3 female) on whom samples were available between the ages of 2 and 28 years, and six sex-matched controls. Approximately 2.5 ml of peripheral blood was collected from each participant using PAXgene Blood RNA Tubes (IVD) (PreAnalytiX GmbH, Hombrechtikon, Switzerland) for RNA extraction according to manufacturer’s instructions. Samples were assessed for RNA quality and quantity by Nanodrop spectrophotometry (NanoDrop, Wilmington, DE, USA). 100ng of total RNA was reverse transcribed using SuperScript VILO cDNA Synthesis Kit (ThermoFisher, Waltham, MA, USA); each sample was prepared in duplicate replicates. Gene cards were run on the QuantStudio 12K Flex Real-Time PCR System (ThermoFisher, Waltham, MA, USA), using amplification conditions entailing: a single cycle of 50°C for 2 minutes, a single cycle of 94.5°C for 10 minutes followed by 40 cycles of 97°C for 30 seconds and 59.7°C for 1 minute. RNA-Seq reads were aligned to the human reference genome (NCBI GRCh38) with Bowtie2 (v 2.3.5.1) in paired-end mode using the ‘local’ and ‘very-sensitive’ presets [34]. Post-processing including conversion to BAM format and sorting were performed with samtools [35]. Reads mapping to known genes were quantified using ht-seq (v 0.6.1p1) [36] with a PHRED quality score cutoff of 10 using the ‘intersection-strict’ model and the un-stranded assignment mode. Differentially expressed genes were identified using edgeR (v 3.8.6) [37]. Briefly, lowly expressed genes were filtered using a counts per million (CPM) cutoff of >2 in > = 10 samples, counts were normalised using the trimmed mean of M-values and dispersion was estimated using built in methods. In order to calculate the power to detect significantly differentially expressed genes in our data we used the R package RnaSeqSampleSize [38]. The function ‘est_power’ was used to perform the power calculation given the sequencing characteristics of our dataset. These sequencing characteristics included; number of samples in each group (n = 6), minimum fold change for prognostic genes (rho = 1.85), total number of genes for testing (m = 12,694), number of expected DE genes (m1 = 187; from our differential expression analysis), false discovery rate (f = 0.01), dispersion of genes (phi0 = 0.1) and average read count for differential expression (lambda0 = 1791). Finally, differentially expressed genes were identified using the exact test and p-values were false discovery rate (FDR) corrected using the method of Benjamini and Hochberg [39]. Genes with an adjusted p-value <0.05 were deemed to be significantly differentially expressed. Differentially expressed (both up/downregulated) genes in affected individuals compared to controls with a log(fold change) >1.5 were used in gene set enrichment analysis [40] of pathway and gene ontology using Reactome [13] and pathways with an entities p value <0.05 were considered significantly overrepresented.

Patient EEG report findings for eight individuals affected with SNIP1-related disorder.

(DOCX)

Click here for additional data file.

ACMG Variant Classification Criteria.

(DOCX)

Click here for additional data file.

Genome-wide SNP mapping in four affected individuals (X:30, X:31, XI:6 and XI:7) identified a single (1.65Mb) region of shared homozygosity, containing 17 genes.

(DOCX)

Click here for additional data file.

Heatmap showing tissue expression levels of the top 50 genes with upregulated expression in individuals with SNIP1-related disorder.

Map created in GTex Portal, Broad Institute 2021.

(DOCX)

Click here for additional data file.

Heatmap showing tissue expression levels of the top 50 genes with downregulated expression in individuals with SNIP1-related disorder.

Map created in GTex Portal, Broad Institute 2021.

(DOCX)

Click here for additional data file.

List of genes that are differentially expressed in individuals with SNIP1-related disorder.

Genes were identified by whole transcriptome sequencing studies of six affected individuals and sex-matched controls, with a false discovery rate (FDR) adjusted p-value of <0.05 and ranked by log fold change (logFC). (A) List of 75 significantly upregulated genes. (B) List of 109 significantly downregulated genes.

(XLSX)

Click here for additional data file.

Genes with an identified clinical association that are up/downregulated in individuals with SNIP1-related disorder.

Tissues expressing each gene, including tissue of highest expression and known clinical associations are detailed. (A) List of 11 genes with an associated clinical phenotype that are upregulated (log fold change (logFC) >1.5) in individuals with SNIP1-related disorder. (B) List of 32 genes with an associated clinical phenotype that are downregulated (log fold change (logFC) <-1.5) in individuals with SNIP1-related disorder. GU; genitourinary, GTC; generalised tonic clonic seizures, SLE; systemic lupus erythematosus, SBH; subcortical band heterotopia, DSD; disorder of sexual development, CRC; colorectal cancer.

(XLSX)

Click here for additional data file.

Differentially expressed (both up/downregulated) gene pathways from Reactome overrepresentation analysis of significantly up/downregulated genes in six affected individuals compared with sex-matched controls and a log(fold change) >1.5 were used in gene set enrichment analysis of pathway and gene ontology.

Pathways with an entities p value <0.05 were considered significantly dysregulated. (A) List of upregulated gene pathways. (B) List of downregulated gene pathways. (C) List of combined dysregulated gene pathways (both up/downregulated). #Entities found: the number of curated molecules that are common between the submitted data set and the named pathway. #Entities total: The total number of curated molecules within the pathway. Entities ratio: The proportion of Reactome pathway molecules represented by this pathway. Calculated as the ratio of entities from this pathway that are found in the submitted data set Vs. all entities within the pathway. Entities pvalue: The result of the statistical test for over-representation: the probability that the overlap between the query and the pathway has occurred by chance. Entities FDR: False discovery rate. Corrected over-representation probability. #Reactions found: The number of reactions in the pathway that are represented by at least one molecule in the submitted data set. #Reactions Total: The number of reactions in the pathway. Reactions ratio: The proportion of Reactome reactions represented by this pathway. Calculated as the ratio of reactions from this pathway that are found within the submitted data set Vs. all Reactome reactions within the pathway. Submitted entities found: genes identified from the submitted list.

(XLSX)

Click here for additional data file.

27 Jul 2021

Dear Dr Crosby,

Thank you very much for submitting your Research Article entitled 'SNIP1 alteration underlies a complex neurodevelopmental disorder' to PLOS Genetics.

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Ammous, et al. describe a large cohort of Amish individuals with homozygous variation affecting one amino acid residue of SNIP1. While two publications have previously associated this gene with a complex NDD (with recognizable clinical features including seizures, craniofacial features, etc.), this paper adds detailed phenotypic data for many additional individuals. The authors also performed RNA-seq on a subset of individuals and suggest pathways involved in pathogenesis. The strengths of the manuscript include detailed phenotypic data for a large cohort, allowing creation of care recommendations. The study also provides a notable (although small) RNA-seq dataset that may aid in additional research opportunities.

My concerns are mostly regarding the novelty of the gene-disease relationship; I would suggest changing the title of the paper to reflect previous work that has been done in this area, and that this is an expansion of that work. Also, it is not clear if the 3 individuals from Puffenberger, et al. were included as part of the 35 here, although it seems like at least one is. Fig1E here looks identical to that of Puffenberger, et al.’s Figure 3B. De-identified images that were covered in the pdf may also be replicated. It would be nice to show data in that Figure from probands other than those that have been previously published, and generally distinguish what was previously done from what is new here.

Other detailed comments:

1. Either add the RefSeq NM and version, or remove the c./p. when just referencing the variant throughout the text. Do leave all the details on p.11, line 196.

2. change “consolidate” in abstract (further support? Solidify?)

3. Overall I would like clarification on the number of individuals and their relatedness. I was a bit confused by the sample numbers at the beginning of the discussion. Why weren’t all 49 individuals who had homozygous SNIP1 variation included? Due to limitations of clinical info? It may be useful to move this summary to the beginning of the results to clarify the population. I like that you mentioned there that these 35 are from 21 interrelated families (p.7, line 120), but maybe mention here a bit more on relatedness of individuals. Something like how many are not first-degree relatives/at least as distant as first cousins/two segregations/etc.

4. “affected with SNIP1-related disorder” (p.7, line 120)…does this mean based on phenotype/clinical features? Would “suspected SNIP1-related disorder” be more accurate?

5. Only a 60% probability of finding significantly differentially expressed genes in RNA-seq seems notably low. Can sample size be increased? (Authors do note that samples size is low.) Did all samples come from that one family in Figure 1F? Is there any possibility of using another individual from a different family?

6. Regarding ClinVar (p.16, line 290): There are other VUSs as well…can you comment on predictions for these (Near NLS, FHA, etc.? Any comment on their frequency in Amish populations? (And frequency of the R111C variant?)

7. Were any other variants of interest identified in WES that were outside of the chr1 region of interest?

8. Have you tried to identify others with variation of interest in SNIP1 through GeneMatcher?

9. It might be nice to mention this variant is rare in gnomAD and TopMed/Bravo, with no homozygous individuals. In gnomAD, 10/11 heterozygotes are in an Amish population.

Reviewer #2: The authors describe in detail clinical findings in 35 individuals from the Amish community with homozygous pathogenic SNIP1 variants (c.1097A>G p.(Glu366Gly)) and define the cardinal features of the disorder. They report also on gene transcript studies in affected individuals. The paper is enjoyable, robust and well written.

The authors claim that they ‘describe extensive genetic studies and clinical findings of a complex inherited neurodevelopmental disorder in 35 individuals associated with a SNIP1 c.1097A>G p.(Glu366Gly) alteration, present at high frequency in the Amish community’. They report that ‘together these data consolidate SNIP1 gene alteration as a cause of an autosomal recessive complex neurodevelopmental disorder and provide important insight into the molecular roles of SNIP1 which likely explain the cardinal clinical outcomes in affected individuals, defining potential therapeutic targets’.

This is not an original gene discovery paper as this gene is already an OMIM morbid gene, the gene is a possible gene in DDG2P and amber on UK PanelApp following work by Puffenberger et al. (2012) which identified exactly the same pathogenic variant identified in this study (c.1097A>G p.(Glu366Gly) and carried out functional work). However, it is an original thorough careful analysis of a large number of affected individuals which gives further very important evidence that biallelic pathogenic SNIP1 variants cause a distinctive disorder (SNIP1 associated syndrome). This will be extremely important for clinicians and scientists researching in the field

The authors claim to have defined therapeutic targets in the abstract, however this isn’t specifically referred to in the discussion (however they have carried out transcript analysis to identify perturbed pathways). This could be misread as meaning a specific molecule or receptor had been identified for targeting as opposed to large pathways which is what I think they are referring to. I think this could be reworded and referred to more clearly in the discussion

The authors have referenced the published literature appropriately and accurately; however, they could make it clearer that the pathogenic variant identified in this report has already been published.

Using ACMG criteria to classify the variant would make this paper better. This would take minimal time (less than one day)

It would have been helpful to give more information about the background of the Amish population and Old Order Amish as this is not given. It would be helpful to clinicians to highlight the spliceosomal aspects of this gene in the abstract so they can place it in context.

It isn’t totally clear how the authors identified the affected individuals. It would be helpful to state How exactly did you identify them? In clinic / examining them through the community? They refer at one point to a historical review of notes and parental survey. More clarity throughout would be helpful to the reader.

The use of ‘alteration’ in the title and paper is not the most accurate scientific/clinical word. Likewise, the title could be improved, and the authors could consider use of ‘SNIP1-associated syndrome’ which they use later in the paper.

With regards to epilepsy, were there any defining aspects of the individuals’ epilepsy. Any EEG abnormalities? Photosensitivity ? febrile seizures Are there any medications that any individuals responded well to? Information about treatment is very helpful to epileptologists.

The authors state several individuals required more than two antiepileptic drugs to achieve ‘reasonable’ seizure control. They don’t state how they defined reasonable seizure control. Do they mean: No seizures? Family reported happy with control? Doctor happy with control? No drop attacks?

The authors state: Individuals identified in late childhood/adolescence are often diagnosed with a mixed tone spastic quadriplegic cerebral palsy. Is this progressive? Why is this not picked up earlier?

The authors state: Other clinical features associated with SNIP1-related disorder include a variable spectrum of congenital cardiac defects (60% of individuals), Are the authors certain that all of these heart defects are all related to SNIP-1 and not due to other homozygous pathogenic variants in other genes? Are isolated heart defects more common in the Amish population than in the general population or not?

There are a small number of typographical errors. Figure 1 looks unfinished, parts A to D are missing. These appear to be clinical photos

**********

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Reviewer #1: Yes

Reviewer #2: No: There is missing data from figure 1 (1a,b,c,d), I understand these are clinical images.

**********

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Reviewer #1: No

Reviewer #2: No

27 Aug 2021

Submitted filename: Response to reviewers_SNIP1_PLOS Genetics.docx

Click here for additional data file.

2 Sep 2021

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We are pleased to inform you that your manuscript entitled "A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder" has been editorially accepted for publication in PLOS Genetics. Congratulations!

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22 Sep 2021

PGENETICS-D-21-00722R1

A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder

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