Is PRRT2 p.Asn98fs (c.291del) pathogenic?

PRRT2 p.Asn98fs (c.291del) is classified Pathogenic in PRRT2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2012-10-01). No gnomAD frequency available for this variant; Associated with seizures, benign familial infantile, 2.

What condition is associated with PRRT2 p.Asn98fs (c.291del)?

PRRT2 p.Asn98fs (c.291del) is associated with seizures, benign familial infantile, 2 (ClinVar).

How common is PRRT2 p.Asn98fs (c.291del) in the general population?

PRRT2 p.Asn98fs (c.291del) 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.Asn98fs

c.291del · rs730882073 · VCV39755

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

seizures, benign familial infantile, 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 2 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.45	GERP 0.31, phastCons 0.036

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.Asn98fs
Coding: c.291del
MANE Select: NM_145239
dbSNP: rs730882073
Type: Deletion
Location: chr16:29813344 (GRCh38)
Gene constraint: LOEUF 0.633 · pLI 0.66 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 51.86
Residue 98: the 'disordered' region

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

Similar variants

PRRT2 p.Arg217fs Pathogenic/Likely pathogenic ★★ same condition
PRRT2 p.Leu171_Ser172insTer Likely pathogenic ★ same condition
PRRT2 p.Val114fs Likely pathogenic ★ same condition
PRRT2 c.-65-1G>A Pathogenic ★ same condition
PRRT2 p.Cys276Tyr Likely pathogenic ★ same condition
PRRT2 c.879+5G>A Pathogenic same condition

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-asn98fs (accessed [today's date]).

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