Is PRRT2 p.Ile318= (c.954C>T) pathogenic?

PRRT2 p.Ile318= (c.954C>T) is classified Likely benign in PRRT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-01). Very rare (popmax 0.00994%, sas).

How common is PRRT2 p.Ile318= (c.954C>T) in the general population?

PRRT2 p.Ile318= (c.954C>T) is very rare (popmax 0.00994%, sas) (gnomAD).

PRRT2 p.Ile318=

c.954C>T · rs764016311 · VCV3067521

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00994%, sas)

⚠ 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 3.3	GERP 1.7, phastCons 1
Overall
CADD	15.63	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00994% South Asian · 9/90,578 alleles

Filtering AF 0.00516% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00377%

Overall 0.00155% 25/1,609,942 alleles · very rare exomes 22/1,457,824 · genomes 3/152,118 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00994%	10,064
Admixed American	0.00168%	59,480
African / African-American	0.00134%	74,816
European (non-Finnish)	0.00119%	84,166

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.Ile318=
Coding: c.954C>T
MANE Select: NM_145239
dbSNP: rs764016311
Type: single nucleotide variant
Location: chr16:29814407 (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-ile318 (accessed [today's date]).

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