Channelopathy-associated congenital insensitivity to pain: genes and variants
Channelopathy-associated congenital insensitivity to pain is linked to 1 analyzed protein (SCN9A). 3 DNA variants are known to cause it; 34 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Also known as: channelopathy-associated congenital insensitivity to pain, autosomal recessive
Genes linked to Channelopathy-associated congenital insensitivity to pain
SCN9A: Sodium channel protein type 9 subunit alpha
The protein forms Nav1.7, a voltage-gated sodium channel that amplifies electrical signals in peripheral sensory neurons. Changes in Nav1.7 activity can produce either excessive pain or congenital insensitivity to pain, making SCN9A central to pain biology.
3 disease-causing and 34 uncertain variants in SCN9A are linked to Channelopathy-associated congenital insensitivity to pain.
Known disease-causing variants in Channelopathy-associated congenital insensitivity to pain
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SCN9A R907Q | 907 | II | Disease-causing (★★) |
| SCN9A C1350R | 1350 | III | Disease-causing |
| SCN9A M1655V | 1655 | IV | Disease-causing |
Same protein, different disease
- Generalized epilepsy with febrile seizures plus is also caused by SCN9A variants; they fall mostly in different places as the Channelopathy-associated congenital insensitivity to pain variants (14 disease-causing).
- Neuropathy, hereditary sensory and autonomic, type 2A is also caused by SCN9A variants; they fall mostly in different places as the Channelopathy-associated congenital insensitivity to pain variants (14 disease-causing).
- Primary erythromelalgia is also caused by SCN9A variants; they fall mostly in different places as the Channelopathy-associated congenital insensitivity to pain variants (6 disease-causing).
- Paroxysmal extreme pain disorder is also caused by SCN9A variants; they fall mostly in different places as the Channelopathy-associated congenital insensitivity to pain variants (4 disease-causing).
Diseases related to Channelopathy-associated congenital insensitivity to pain
- Amyotrophic lateral sclerosis, also linked to SCN9A
- Generalized epilepsy with febrile seizures plus, also linked to SCN9A
- Cardiac arrhythmia, also linked to SCN9A
- Epilepsy, also linked to SCN9A
- Neuropathy, hereditary sensory and autonomic, type 2A, also linked to SCN9A
- Primary erythromelalgia, also linked to SCN9A
- Paroxysmal extreme pain disorder, also linked to SCN9A
- Focal epilepsy, also linked to SCN9A
- Lennox-Gastaut syndrome, also linked to SCN9A
Frequently asked questions
Which genes are linked to Channelopathy-associated congenital insensitivity to pain?
In CATVariant, Channelopathy-associated congenital insensitivity to pain is linked to 1 analyzed protein: SCN9A (Sodium channel protein type 9 subunit alpha).
How many genetic variants are linked to Channelopathy-associated congenital insensitivity to pain?
39 variants: 3 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 34 are of uncertain significance or have conflicting reports.
Which uncertain variants in Channelopathy-associated congenital insensitivity to pain look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
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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