Sugi Variant
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PRRT2/p.Ile329del

PRRT2 p.Ile329del

c.979ATC[2] · rs1057518374 · VCV373365

Uncertain significance Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00169%, amr)

⚠ 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
ConservationphyloP 7.6GERP -3.4, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes
Grpmax group 0.00169% Admixed American · 1/59,122 alleles
Overall 6.23e-05% 1/1,606,384 alleles · very rare exomes 1/1,454,166 · genomes 0/152,218 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene
PRRT2
Protein
p.Ile329del
Coding
c.979ATC[2]
MANE Select
NM_145239
dbSNP
rs1057518374
Type
Microsatellite
Location
chr16:29814430 (GRCh38)
Full PRRT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-ile329del (accessed [today's date]).

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