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SCN9A gene

Reviewed by Medicinsk Expert•Last updated: 2026-10-22•Gene

SCN9A gene

The SCN9A gene provides instructions for making a sodium channel that is essential for transmitting pain signals and the sense of smell.

Normal Function

The SCN9A gene belongs to a family of genes that provide instructions for making sodium channels. These channels, which transport positively charged sodium atoms (sodium ions) into cells, play a key role in a cell's ability to generate and transmit electrical signals.

The SCN9A gene provides instructions for making one part (the alpha subunit) of a sodium channel called NaV1.7. NaV1.7 sodium channels are found in nerve cells called nociceptors. Nociceptors are part of the peripheral nervous system, which connects the brain and spinal cord to cells that detect sensations such as touch, smell, and pain. Nociceptors are primarily involved in transmitting pain signals. NaV1.7 sodium channels are also found in olfactory sensory neurons, which are nerve cells in the nasal cavity that transmit smell-related signals to the brain.

Health Conditions Related to Genetic Changes

Channelopathy-associated congenital insensitivity to pain

Multiple variants in the SCN9A gene have been found to cause channelopathy-associated congenital insensitivity to pain, a condition that inhibits the ability to perceive physical pain. Most of these SCN9A gene variants result in the production of a nonfunctional alpha subunit of the NaV1.7 sodium channel. These nonfunctional subunits do not allow NaV1.7 sodium channels to open, preventing the flow of sodium ions into nociceptors. This lack of sodium ions blocks nociceptors from transmitting pain signals from the site of an injury to the brain. The loss of NaV1.7 sodium channel activity in olfactory sensory neurons likely prevents smell-related signals from reaching the brain, leading to a complete loss of the sense of smell (anosmia).

Erythromelalgia

Multiple variants in the SCN9A gene have been found to cause erythromelalgia, a condition characterized by episodes of pain, redness, and swelling in various parts of the body, particularly the hands and feet. All the identified variants change one protein building block (amino acid) in the NaV1.7 sodium channel. These variants cause cells to produce NaV1.7 sodium channels that open more easily and stay open longer than normal, increasing the flow of sodium ions. This increase in sodium ions enhances the transmission of pain signals, leading to the signs and symptoms of erythromelalgia.

Paroxysmal extreme pain disorder

Multiple variants in the SCN9A gene have been found to cause paroxysmal extreme pain disorder. This condition is characterized by severe pain attacks accompanied by skin redness and warmth (flushing) and, sometimes, seizures and changes in breathing and heart rate. The variants that cause this condition change single amino acids in the alpha subunit of the NaV1.7 sodium channel. As a result, the sodium channel does not completely close when it is turned off, allowing sodium ions to flow abnormally into nociceptors. This increase in sodium ions enhances the transmission of pain signals.

Small fiber neuropathy

Variants in the SCN9A gene account for approximately 30 percent of cases of small fiber neuropathy, a condition characterized by severe pain attacks and a reduced ability to differentiate between hot and cold. The variants that cause this condition change single amino acids in the alpha subunit of the NaV1.7 sodium channel. As a result, the sodium channel does not completely close when it is turned off, allowing sodium ions to flow abnormally into nociceptors. This increase in sodium ions enhances the transmission of pain signals. In people with this condition, the axons that extend from the nociceptors and transmit pain signals degenerate over time.

Other disorders

At least three variants in the SCN9A gene have been found in a group of people with febrile seizures, which are seizures that are triggered by a high fever. When febrile seizures are associated with variants in the SCN9A gene, the condition is known as familial febrile seizures 3B. Variants in the SCN9A gene, when coupled with variants in another gene called SCN1A, can alter the progression of a seizure disorder called Dravet syndrome, making the signs and symptoms more severe.

Other Names for This Gene

  • hNE
  • Nav1.7
  • NE-NA
  • NENA
  • PN1
  • SCN9A_HUMAN
  • sodium channel, voltage gated, type IX alpha subunit
  • sodium channel, voltage-gated, type IX, alpha
  • sodium channel, voltage-gated, type IX, alpha polypeptide
  • sodium channel, voltage-gated, type IX, alpha subunit
  • voltage-gated sodium channel alpha subunit Nav1.7

Frequently Asked Questions

The inability to feel pain, while seemingly beneficial, poses significant risks. Individuals with CIP are prone to severe injuries, infections, and even life-threatening conditions because they lack the crucial warning system that pain provides. They may not notice fractures, burns, deep cuts, or internal injuries, leading to delayed treatment, chronic damage to joints and bones, and severe infections. Regular medical check-ups and careful monitoring are essential.
Daily life precautions are critical to prevent injury. This includes frequent self-checks for cuts, bruises, or swelling, especially on hands and feet. Avoiding extreme temperatures, wearing protective gear during activities, and ensuring a safe home environment (e.g., childproofing for adults) are important. Regular dental check-ups are also vital as dental pain won't be felt. Education for caregivers and family about these risks is also crucial.
Diagnosis often begins with a clinical history of repeated injuries without pain sensation, usually starting in infancy or early childhood. A thorough physical examination will look for signs of unnoticed injuries or joint damage. Genetic testing for mutations in the SCN9A gene is the definitive diagnostic method, confirming the presence of variants known to cause CIP. Nerve conduction studies might also be performed, though they typically show normal results.
Currently, there is no cure for CIP itself, as it's a genetic condition affecting nerve function. Treatment focuses entirely on managing and preventing complications from the lack of pain sensation. This involves proactive injury prevention, vigilant monitoring for unnoticed injuries, and prompt treatment of any wounds or infections. Unfortunately, there is no specific treatment to restore the sense of smell lost due to the SCN9A mutation.
Source: MedlinePlus, National Library of Medicine

MedlinePlus brings together authoritative health information from the National Library of Medicine (NLM), the National Institutes of Health (NIH), and other government agencies and health-related organizations.