Is PRRT2 p.Ala84fs (c.250del) pathogenic?

PRRT2 p.Ala84fs (c.250del) is classified Pathogenic/Likely pathogenic in PRRT2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-11-01). No gnomAD frequency available for this variant; Associated with seizures, benign familial infantile, 2.

What condition is associated with PRRT2 p.Ala84fs (c.250del)?

PRRT2 p.Ala84fs (c.250del) is associated with seizures, benign familial infantile, 2 (ClinVar).

How common is PRRT2 p.Ala84fs (c.250del) in the general population?

PRRT2 p.Ala84fs (c.250del) is no gnomAD frequency available for this variant (gnomAD).

How is Self-limited infantile epilepsy inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

PRRT2 p.Ala84fs

c.250del · rs2142423353 · VCV1694791

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

seizures, benign familial infantile, 2

⚠ 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.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.3	GERP -0.99, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Ala84fs
Coding: c.250del
MANE Select: NM_145239
dbSNP: rs2142423353
Type: Deletion
Location: chr16:29813303 (GRCh38)

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

Disease context

seizures, benign familial infantile, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Self-limited infantile epilepsy (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy, Neonatal

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-ala84fs (accessed [today's date]).

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