SYNGAP1 encephalopathy

Cohort

Fifty-seven patients (53% male, median age at study 8 years) with (likely) pathogenic SYNGAP1 variants were included: 34 truncating, 8 splice-site, and 11 missense/in-frame mutations and 4 microdeletions. Forty-six (81%) patients have not been previously reported. Thirty-nine of these patients had novel mutations, which included a total of 35 unique mutations because 4 were recurrent. The remaining 7 individuals had previously reported mutations. Figure 1A depicts the 57 SYNGAP1 mutations and microdeletions found in our patient cohort, and figure 1B shows the 62 SYNGAP1 variants of all previously reported patients who were not included in our cohort.^{1,2,4,–,8,17,–,28} Inheritance was tested in 53 of 57 patients, and the mutation had arisen de novo in all. Table 1 describes the clinical features for our cohort according to the 4 genotypic groups. More detailed individual genetic and phenotypic are summarized in tables e-1 and e-2 (available from Dryad, doi.org/10.5061/dryad.ck70sj0).

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Figure 1 Schematic presentation of SYNGAP1 mutations and microdeletions (A) in patients of our cohort or (B) previously published in the literature

Chromosome 6p21.32 microdeletions including SYNGAP1, are presented as gray bars with << and >> indicating that their breakpoints were outside the region presented here. Truncating (◆) and splice-site (→) mutations are presented above the gene, and missense and in-frame (•) mutations are shown underneath the gene. Bold variants concern recurrent variants that were identified in our cohort but also previously published in the literature. Colors of the lines represent the epilepsy syndrome phenotype: moderate to severe developmental and epileptic encephalopathy (red), moderate to severe developmental encephalopathy with epilepsy (orange), moderate to severe developmental encephalopathy with no epilepsy (blue), mild developmental and epileptic encephalopathy (light green), mild developmental encephalopathy with no epilepsy (dark green), and unknown/unclassified epilepsy (gray). Chromosomal coordinates were based on National Center for Biotechnology Information Build 37 [hg19] and SYNGAP1 mutations, protein domains, and exons on the longest isoform 1 (NM_006772.2).

Seizure types

Fifty-six of 57 patients had epilepsy with a median age at seizure onset of 2 years (range 4 months–7 years, known in 55). At onset, 50 patients had generalized seizures, 1 had infantile spasms in the context of West syndrome, 3 had possible focal seizures, and 2 had unknown seizure types.

Absence seizures occurred in 53 of 57 (93%) patients: eyelid myoclonia (EM) with absences in 37, atypical absences in 11, typical absences in 10, and myoclonic absences in 2. Other seizure types included myoclonic (19 of 57, 33%), atonic (8 of 57, 12%), myoclonic-atonic (3 of 57, 5%), and unclassified drop attacks (2 of 57, 4%). Fourteen (25%) patients had tonic-clonic seizures (TCS), of whom 2 also had focal seizures. Five patients had focal seizures without TCS. Four of 57 (7%) patients had febrile seizures before epilepsy onset.

Reflex seizures were seen, often occurring in clusters, and triggered by eating (25%), sound (7%), or touch (4%). Hunger was also associated with seizures in 7%. Clinical photosensitivity occurred in 13 (23%) patients and EEG photosensitivity in 17 of 31 (55%) tested. Three (5%) patients had self-induced seizures with hyperventilation.

Novel seizure type: EM-myoclonic-atonic seizures

Of the 36 patients with EM, we observed a novel seizure type in 13 of 36 (36%) in whom the EM evolved to a drop attack. The nature of the drop attack was an EM-myoclonic-atonic seizure in 5 and an EM-atonic seizure in 8 patients (video 1). Ictal EEG showed generalized spike wave (GSW) discharges coinciding with the EM, followed by a spike-wave complex correlating with the myoclonic (spike) and atonic (slow wave) component (figure 2). We also observed that EM seizures were accompanied by myoclonic jerks of the limbs in 4 of 36 (11%) patients. These novel seizure types, EM-myoclonic-atonic and EM-atonic, occurred mainly when EM clustered and at times of poor seizure control.

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Figure 2 Ictal EEG registration during eyelid myoclonia–myoclonic–atonic seizure

Red arrows indicate the different phases of the seizure associated with a generalized spike wave (eyelid myoclonia) and a further spike wave correlating with the myoclonic (spike) and atonic (wave) components.

Neurodevelopment and behavioral issues

Developmental delay was identified soon after birth in 55 of 56 (96%) patients and preceded seizure onset in all. Development regressed or plateaued with seizure onset in 56 patients. Language was severely impaired, with 12 patients being nonverbal, at age 2 to 33 years. ID was present in 55 of 57 patients, being moderate to severe in 50 and mild in 5.

Behavioral problems were seen in 41 of 56 (73%) patients and were often severe with oppositional and defiant behavior with aggression, self-injury, and tantrums. ASD was diagnosed in 30 (53%) patients.

Other features

An interesting observation was that the families of 39 of 54 (72%) patients noted that they had a high pain threshold. Patients did not respond to painful events such as a fractured bone, surgical incision of a lesion, or a foreign object lodged in their foot.

Difficulties with eating were a major problem in 39 (68%) patients. Twenty-three patients had a poor intake because they were fussy about food type, color, texture, and temperature (16) or had oral aversion (5), oral hypersensitivity (3), and poor appetite (3). Four patients needed a nasogastric tube because of the severity of their eating problems. In contrast, 7 patients had uncontrolled eating with gorging, and 3 would eat inedible objects. Eleven of 55 patients had difficulties with transition from fluids to solid food in early childhood. Seventeen of 56 patients had chewing and swallowing difficulties.

Sleep was disturbed in 34 of 55 (62%) patients with difficulties initiating (n = 19) and maintaining (n = 29) sleep. Improved seizure control led to better sleep in 12 patients. There was no clear correlation with EEG features; there was an increase in epileptiform activity in sleep in 9 of 23 (39%) patients with sleep difficulties, which was also observed in 6 of 12 (50%) without sleep difficulties. Sleep also improved with melatonin (n = 10), clonidine (n = 5), and trazodone (n = 1).

Examination findings

Photographs of 31 of 57 patients were available (figure 3) and revealed subtle dysmorphic features, not present in all patients. These included full, slightly prominent eyebrows with medial flaring in some; hypertelorism; full nasal tip, slightly upturned nasal tip in younger children; short philtrum; cupid bow upper lip; broad mouth with diastemata of the upper teeth; and small pointed chin.

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Figure 3 SYNGAP1 dysmorphology

Portrait photographs from 31 of 56 patients with SYNGAP1 mutations or microdeletions including SYNGAP1. (A) Patient 4, (B) patient 6, (C) patient 7, (D), patient 8 (sibling of patient 9), (E) patient 9 (sibling of patient 8), (F) patient 12, (G) patient 13, (H) patient 14, (I) patient 16, (J) patient 18, (K) patient 19, (L) patient 20, (M) patient 21, (N) patient 23, (O) patient 25, (P) patient 27, (Q) patient 28, (R) patient 29, (S) patient 31, (T) patient 32, (U) patient 33, (V) patient 34, (W) patient 35, (X) patient 37, (Y) patient 45, (Z) patient 47, (AA) patient 50, (AB) patient 51, (AC) patient 52, (AD) patient 54 (monozygotic twin with patient 55), and (AE) patient 55 (monozygotic twin with patient 54).

Neurologic examination showed hypotonia in 38 (67%), ataxia or an unsteady gait in 29 (51%), tremor in 5 (9%), and microcephaly in 1 (2%) of 54. Orthopedic abnormalities included foot or spine deformities in 16 (28%), including pes planus (7), pronated feet (4), scoliosis (3), pes cavus (1), congenital hip dislocation (1), or congenital hip dysplasia (1).

EEG findings

EEG results were available for 52 of 57 patients from when their epilepsy was active. Many children did not have further EEGs because of severe behavioral problems. GSW and generalized poly-spike wave were reported in 39 of 52 (75%) patients. Focal or multifocal epileptiform discharges were seen in 28 of 52 (54%), often in addition to GSW or generalized poly-spike wave (21 of 39, 54%). Slow background activity was seen in 26 of 52 (50%) patients.

Neuroimaging

MRI was reported as normal in 37 of 53 (70%) patients. One patient had a left frontal subcortical nodular heterotopia. The 15 remaining patients had nonspecific findings: thin corpus callosum (3; 2 of 3 also had a thin chiasma opticum), enlarged ventricles or subarachnoid spaces (3), hyperintense T2 signals in the white matter (3), posterior centrum semiovale (2) or fasciculus longitudinalis medialis (1), patent cavum vergae (1), atypical white matter abnormalities (1), mega cisterna magna fossa posterior (1), discrete hippocampal tissue loss (1), or a pineal cyst (1).

Brain pathology

Brain pathology was available from patient 14, a 33-year-old nonverbal woman with a de novo SYNGAP1 nonsense mutation (video 2), who died of aspiration pneumonia. The pathology showed cerebellar Purkinje cell loss with associated astrocytosis (figure 4A). Astrocytosis was found predominantly in the superficial cortical layer but also in the hippocampi and deep gray nuclei (figure 4B). Macroscopic evaluation showed a low brain weight (1,194 g, −3.2 SD) with widely but moderately distributed leptomeningeal fibrosis, most evident over the frontal lobes (figure 4C). Cortical neurons did not show evidence of anoxic ischemic injury (data not shown).

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Figure 4 Brain pathology in a patient with an SYNGAP1 mutation

(A) Glial fibrillary acidic protein (GFAP)–stained section of the cerebellar cortex showing a single surviving Purkinje cell (arrow points toward this cell) in a field of Purkinje cell loss and mild internal granular layer and cerebellar molecular layer astrocytosis. (B) GFAP staining of dentate gyrus showing no neuronal loss but mild reactive astrocytosis in the dentate granular layer and the dentate molecular layer of the hippocampus. (C) Vertex view of the cerebral hemispheres showing leptomeningeal fibrosis.

Epilepsy syndrome

A distinctive generalized epilepsy phenotype emerged combining features of 2 well-described syndromes, epilepsy with eyelid myoclonia with absences, reported by Jeavons,³⁶ and epilepsy with myoclonic-atonic seizures, described by Doose et al.³⁷ The overall gestalt in 56 of 57 patients was a spectrum of severity of generalized DEE with multiple seizure types, including EM, myoclonic, and atonic (and combinations of all 3). TCS were fairly frequent, whereas focal seizures occurred in a minority. The majority of patients had a severe outcome with moderate to severe ID (49 of 56, 88%), while 7 of 56 (12%) had a milder outcome with normal intellect or mild ID. One child with a mild outcome had West syndrome. The remaining patient with no seizures but epileptiform abnormalities on EEG had a (static) developmental encephalopathy with a severe outcome. Another distinctive feature of SYNGAP1, seen in a quarter of cases, was the presence of reflex seizures triggered by eating.

Epilepsy treatment and outcome

Overall, 20 different antiepileptic drugs (AEDs) were started (table e-3, available from Dryad, doi.org/10.5061/dryad.ck70sj0). Valproate and lamotrigine were most commonly prescribed (n = 45 and n = 22), with ongoing prescription of lamotrigine for 77% of patients and valproate for 64% patients. Of the 6 patients who had received cannabidiol, 5 of 6 (83.3%) remained on it.

Thirty-five of 56 (63%) patients had refractory epilepsy with ongoing seizures after 2 AEDs. Six became seizure-free on the third to sixth AED. In total, 10 of 56 (18%) patients became seizure-free at 7 years of age (median, range 3–13 years). Of these, seizures were controlled on monotherapy with valproate (3), levetiracetam (1), or steroids (1, for infantile spasms). Polytherapy combinations resulting in seizure freedom included levetiracetam and topiramate (1), valproate and lamotrigine (1), and cannabidiol, valproate, and lamotrigine (1). Two were seizure-free on no treatment. Four patients had no seizures for a period of 6 months to 7 years while treated with carbamazepine (1), lamotrigine (1), valproate (1), or valproate, lamotrigine, and clobazam, but seizures recurred.

Genotype-phenotype correlation

The phenotypes of patients with truncating, splice-site, or missense/in-frame mutations and microdeletions were similar overall, except that 4 patients with microdeletions all had an earlier seizure onset (20 months compared with 2 years in the remaining cohort, table 1). All 4 patients had microdeletions that included additional genes (4–13 genes). In terms of the outcome, all 4 cases had severe ID, consistent with the rest of the cohort. Given their similar epileptology and other features (high pain threshold in 2, poor oral intake in 2, seizures triggered by hunger and photosensitivity in 1, and dysmorphic features in 2), we included them in the total cohort.

For evaluating genotype-phenotype correlations, we separated SYNGAP1 encephalopathies into 2 groups based on severity determined by their intellect. Milder phenotypes included normal intellect or mild ID; severe phenotypes referred to moderate to severe ID. Of the 7 patients with a milder phenotype (green mutations, figure 1A), 5 had a truncating or splice-site mutation, of which 4 were located in exons 1 to 4. Two other patients had a missense variant in exons 6 and 11. Five previously reported patients also had a milder phenotype (green and dark green mutations, figure 1B), with 3 of 5 having mutations in exons 1 to 4. In the combined cohort of our and previously reported patients, milder phenotypes were significantly more often observed in patients with mutation or deletions in exons 1 to 4 (50%, n = 6 of 12) compared to exons 5 to 19 (7%, 6 of 85, p = 0.001, Fisher exact test). No significant differences were observed in outcome between patients with different mutation types (data not shown).

Patients with SYNGAP1 variants of unknown significance (n = 5)

Not included in our cohort of 56 patients were 5 individuals with an SYNGAP1 variant of unknown significance. Tables e-1 and e-2 (available from Dryad, doi.org/10.5061/dryad.ck70sj0) show details of their pathogenicity predictions and associated phenotypes. Three patients who had variants reported in gnomAD or ExAC and for whom inheritance of their SYNGAP1 variant was unavailable had phenotypes that were consistent with our large cohort.³⁸ Two had generalized DEE and 1 had mild ID with EM. Their presence in population databases is difficult to explain, although EM can be subtle and easily missed. It remains to be determined whether their SYNGAP1 variant has a role in their presentation. The remaining 2 had variants with lower conservation and pathogenicity prediction scores and had focal epilepsy with or without ID, so their phenotype was quite different.