Benign neonatal seizures: genes and variants
Benign neonatal seizures is linked to 1 analyzed protein (KCNQ3). 13 DNA variants are known to cause it; 414 more are uncertain, and 1 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Benign neonatal seizures
KCNQ3: Potassium voltage-gated channel subfamily KQT member 3
Together with KCNQ2, its slowly activating current provides much of the neuronal M-current that suppresses repetitive firing. Pathogenic variants can cause self-limited neonatal epilepsy or more severe developmental and epileptic encephalopathy.
13 disease-causing and 414 uncertain variants in KCNQ3 are linked to Benign neonatal seizures.
Where Benign neonatal seizures variants cluster
- KCNQ3 Segment S6 (positions 327–353): 3 of 13 disease-causing changes, 7.5× more than its size predicts.
Known disease-causing variants in Benign neonatal seizures
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| KCNQ3 R330C | 330 | Segment S6 | Disease-causing (★★) |
| KCNQ3 R330H | 330 | Segment S6 | Disease-causing (★★) |
| KCNQ3 R364H | 364 | Mediates interaction with calmodulin | Disease-causing (★★) |
| KCNQ3 R230C | 230 | Segment S4 | Disease-causing (★★) |
| KCNQ3 A306V | 306 | Segment H5 | Disease-causing (★★) |
| KCNQ3 I317T | 317 | Selectivity filter | Disease-causing (★★) |
| KCNQ3 R330L | 330 | Segment S6 | Disease-causing (★) |
| KCNQ3 R364C | 364 | Mediates interaction with calmodulin | Disease-causing (★) |
| KCNQ3 G310D | 310 | Segment H5 | Disease-causing (★) |
| KCNQ3 I317M | 317 | Selectivity filter | Disease-causing (★) |
| KCNQ3 G268R | 268 | Segment S5 | Disease-causing (★) |
| KCNQ3 A375T | 375 | Mediates interaction with calmodulin | Disease-causing (★) |
| KCNQ3 M237K | 237 | Segment S4 | Disease-causing (★) |
Uncertain variants in Benign neonatal seizures that look disease-causing
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| KCNQ3 A306T | 306 | Segment H5 | Uncertain (★) | +6: in a 3D region that tolerates change poorly (2A); A306V at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.96 |
Which prediction tools work for Benign neonatal seizures
How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).
- CATVariant: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- PolyPhen-2: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 98 out of 100
Same protein, different disease
- Seizures, benign familial neonatal, 1 is also caused by KCNQ3 variants; they fall partly in the same places as the Benign neonatal seizures variants (7 disease-causing).
Diseases related to Benign neonatal seizures
- Seizures, benign familial infantile, 3, also linked to KCNQ3
- Seizures, benign familial neonatal, 1, also linked to KCNQ3
- Epilepsy, also linked to KCNQ3
- Self-limited epilepsy with centrotemporal spikes, also linked to KCNQ3
Frequently asked questions
Which genes are linked to Benign neonatal seizures?
In CATVariant, Benign neonatal seizures is linked to 1 analyzed protein: KCNQ3 (Potassium voltage-gated channel subfamily KQT member 3).
How many genetic variants are linked to Benign neonatal seizures?
450 variants: 13 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 414 are of uncertain significance or have conflicting reports.
Which uncertain variants in Benign neonatal seizures look disease-causing?
1 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example KCNQ3 A306T. These are leads for expert review, not diagnoses.
Which variant effect predictor works best for Benign neonatal seizures?
Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.98, based on 12 disease-causing and 20 harmless variants).
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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