Primary erythermalgia: genes and variants
Explore variant evidence for Primary erythermalgia across 1 analyzed protein (SCN9A). Linked ClinVar records include 6 pathogenic or likely pathogenic variants, 29 variants of uncertain significance and 6 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Source labels are pooled across this disease family.
Data updated 2026-10-10. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Primary erythermalgia
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.
6 ClinVar pathogenic / likely pathogenic and 35 uncertain variants in SCN9A have source records linked to Primary erythermalgia. Association strength is not clinical gene validity.
Where Primary erythermalgia variants cluster
- SCN9A S5 of repeat II (positions 866–888): 3 of 6 ClinVar pathogenic / likely pathogenic variants, 43.2× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Primary erythermalgia
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SCN9A L869H | 869 | II | Pathogenic / likely pathogenic (★★) |
| SCN9A L834R | 834 | II | Pathogenic / likely pathogenic (★) |
| SCN9A Q886E | 886 | II | Pathogenic / likely pathogenic (★) |
| SCN9A L869F | 869 | II | Pathogenic / likely pathogenic |
| SCN9A F1460V | 1460 | III | Pathogenic / likely pathogenic |
| SCN9A F216S | 216 | I | Pathogenic / likely pathogenic |
Same protein, different disease
- Generalized epilepsy with febrile seizures plus also has ClinVar records linked to SCN9A variants; they fall mostly in different places as the Primary erythermalgia variants (14 pathogenic / likely pathogenic).
- Neuropathy, hereditary sensory and autonomic, type 2A also has ClinVar records linked to SCN9A variants; they fall mostly in different places as the Primary erythermalgia variants (14 pathogenic / likely pathogenic).
- Paroxysmal extreme pain disorder also has ClinVar records linked to SCN9A variants; they fall mostly in different places as the Primary erythermalgia variants (4 pathogenic / likely pathogenic).
- Channelopathy-associated congenital insensitivity to pain also has ClinVar records linked to SCN9A variants; they fall mostly in different places as the Primary erythermalgia variants (3 pathogenic / likely pathogenic).
Diseases related to Primary erythermalgia
- 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
- Paroxysmal extreme pain disorder, also linked to SCN9A
- Focal epilepsy, also linked to SCN9A
- Channelopathy-associated congenital insensitivity to pain, also linked to SCN9A
- Migraine, also linked to SCN9A
- Lennox-Gastaut syndrome, also linked to SCN9A
Frequently asked questions
Which genes have records linked to Primary erythermalgia?
This view contains 1 analyzed proteins: SCN9A. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 6 pathogenic or likely pathogenic variants, 29 variants of uncertain significance and 6 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 0 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 49 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses 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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