PRRT2 (Q7Z6L0) variants and mutations

PRRT2 (also known as Q7Z6L0) is a human protein-coding gene encoding a proline-rich transmembrane protein 2 protein. It modulates presynaptic neurotransmitter release and neuronal excitability through interactions with SNARE machinery and ion channels. Haploinsufficiency commonly causes paroxysmal kinesigenic dyskinesia, self-limited infantile seizures, or the combined infantile-convulsions-and-choreoathetosis phenotype. This analysis covers 980 PRRT2 variants and mutations. Of these, 82% have computational variant effect predictions. Disease context includes episodic kinesigenic dyskinesia 1, infantile convulsions and choreoathetosis, and benign familial infantile epilepsy. Example PRRT2 variants include A2E, A2T, and A3G.

Variant analysis overview

Gene: PRRT2
Protein: Q7Z6L0
UniProt accession: Q7Z6L0
Organism: Homo sapiens
Variants analyzed: 980
Variant scope: all variants
Completed: 2026-08-18

Variant and mutation evidence

Variant composition: 633 unspecified-consequence records; 151 missense variants; 158 synonymous variants; 8 in-frame deletions; 17 frameshift variants; 4 stop-gained variants; 2 in-frame insertions; 1 stop lost; 1 stop retained variant; 5 substitution
Prediction scores: 803 variants have prediction scores (82% of the analyzed set).

Clinical, disease, and population context

Disease context: 25 disease associations are represented. Top associations: episodic kinesigenic dyskinesia 1, infantile convulsions and choreoathetosis, benign familial infantile epilepsy, episodic kinesigenic dyskinesia, hereditary disease, Seizure, PRRT2-associated paroxysmal movement disorder, neurodegenerative disease, autosomal recessive non-syndromic intellectual disability, Paroxysmal exertion-induced dyskinesia, familial or sporadic hemiplegic migraine, paroxysmal nonkinesigenic dyskinesia.

Protein structure and variant hotspots

Protein features: 1 transmembrane segments; 6 post-translational modification sites.
Structural context: 48 variants have structural context.
PTM context: 17 variants overlap post-translational modification sites.

Data sources

Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.

Notable PRRT2 variants

Examples include A2E, A2T, A3G, A3V, A3D, S4G, S4R, S4S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.

PRRT2 analysis run — PRRT2 (980 variants) — completed 2026-08-18