Table. 2 Phenotypic terms associated with PTV and missense variants (n = 409).
From: Computational analysis of 10,860 phenotypic annotations in individuals with SCN2A-related disorders
HPO term | HPO code | P value | Odds ratio (95% CI) | Frequency |
|---|---|---|---|---|
PTV | ||||
Behavioral abnormality | HP:0000708 | 4.07×10-14 | 8.61 (4.57–17.01) | 0.76 |
Autism | HP:0000717 | 1.06×10-13 | 8.16 (4.49–15.13) | 0.63 |
Autistic behavior | HP:0000729 | 2.31×10-13 | 7.76 (4.26–14.50) | 0.68 |
Stereotypy | HP:0000733 | 1.30×10-5 | 5.49 (2.45–12.22) | 0.24 |
Sleep disturbance | HP:0002360 | 1.43×10-5 | 7.04 (2.76–18.32) | 0.19 |
Childhood onset | HP:0011463 | 0.0004 | 3.57 (1.71–7.29) | 0.25 |
Delayed speech and language development | HP:0000750 | 0.0005 | 3.72 (1.70–7.96) | 0.22 |
Intellectual disability, moderate | HP:0002342 | 0.0013 | 3.83 (1.59–8.94) | 0.18 |
Neurodevelopmental abnormality | HP:0012759 | 0.0023 | 2.58 (1.35–5.24) | 0.79 |
Short attention span | HP:0000736 | 0.0047 | 3.83 (1.38–10.20) | 0.13 |
Hyperactivity | HP:0000752 | 0.0047 | 3.83 (1.38–10.20) | 0.13 |
Attention deficit–hyperactivity disorder | HP:0007018 | 0.0047 | 3.83 (1.38–10.20) | 0.13 |
Involuntary movements | HP:0004305 | 0.01 | 2.65 (1.30–5.25) | 0.25 |
Missense | ||||
Neonatal onset | HP:0003623 | 4.69×10-14 | Inf (11.88–Inf) | 0.40 |
Seizures | HP:0001250 | 3.71×10-13 | 8.91 (4.77–16.83) | 0.89 |
Epileptic spasms | HP:0011097 | 1.44×10-6 | Inf (4.39–Inf) | 0.20 |
Infantile spasms | HP:0012469 | 2.62×10-6 | Inf (4.15–Inf) | 0.19 |
Infantile onset | HP:0003593 | 3.77×10-6 | 11.44 (2.93–98.45) | 0.26 |
Interictal epileptiform activity | HP:0011182 | 8.29×10-6 | 3.71 (1.97–7.38) | 0.51 |
Focal-onset seizure | HP:0007359 | 1.61×10-5 | 4.08 (1.98–9.26) | 0.41 |
Interictal EEG abnormality | HP:0025373 | 2.85×10-5 | 3.42 (1.83–6.68) | 0.51 |
Abnormal nervous system electrophysiology | HP:0001311 | 6.00×10-5 | 3.09 (1.70–5.80) | 0.55 |
EEG abnormality | HP:0002353 | 6.00×10-5 | 3.09 (1.70–5.80) | 0.55 |
Abnormality of CNS electrophysiology | HP:0030178 | 6.00×10-5 | 3.09 (1.70–5.80) | 0.55 |
Hypsarrhythmia | HP:0002521 | 0.0001 | Inf (2.88–Inf) | 0.14 |
EEG with burst suppression | HP:0010851 | 0.0002 | 13.69 (2.27–558.40) | 0.17 |
Generalized-onset seizure | HP:0002197 | 0.0005 | 2.77 (1.50–5.34) | 0.48 |
EEG with focal epileptiform discharges | HP:0011185 | 0.0008 | 3.20 (1.50–7.61) | 0.33 |
EEG with generalized epileptiform discharges | HP:0011198 | 0.0014 | 3.02 (1.46–6.88) | 0.34 |
Multifocal epileptiform discharges | HP:0010841 | 0.0019 | 4.27 (1.51–16.70) | 0.21 |
Encephalopathy | HP:0001298 | 0.0030 | 2.59 (1.31–5.53) | 0.36 |
Generalized tonic seizures | HP:0010818 | 0.0030 | 4.20 (1.48–16.41) | 0.21 |
Epileptic encephalopathy | HP:0200134 | 0.0065 | 2.50 (1.26–5.32) | 0.35 |
Focal tonic seizures | HP:0011167 | 0.0077 | 5.39 (1.35–46.94) | 0.14 |
Abnormality of the cerebrum | HP:0002060 | 0.01 | 2.84 (1.23–7.65) | 0.25 |
