Is PRRT2 p.Ala197= (c.591C>T) pathogenic?

PRRT2 p.Ala197= (c.591C>T) is classified Likely benign in PRRT2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-01). No allele count reported in gnomAD v4.1 (AN 1,612,654); Associated with episodic kinesigenic dyskinesia.

What condition is associated with PRRT2 p.Ala197= (c.591C>T)?

PRRT2 p.Ala197= (c.591C>T) is associated with episodic kinesigenic dyskinesia (ClinVar).

How common is PRRT2 p.Ala197= (c.591C>T) in the general population?

PRRT2 p.Ala197= (c.591C>T) is no allele count reported in gnomAD v4.1 (AN 1,612,654) (gnomAD).

How is Paroxysmal kinesigenic dyskinesia inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

PRRT2 p.Ala197=

c.591C>T · rs958471607 · VCV1653562

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,654)

Conditions

episodic kinesigenic dyskinesia

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.1	GERP -1.1
Overall
CADD	4.132	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,612,654). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PRRT2
Protein: p.Ala197=
Coding: c.591C>T
MANE Select: NM_145239
dbSNP: rs958471607
Type: single nucleotide variant
Location: chr16:29813645 (GRCh38)

Full PRRT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

episodic kinesigenic dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Paroxysmal kinesigenic dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (Worldwide)

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/prrt2-p-ala197 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown