Is PRRT2 p.Pro144= (c.432C>T) pathogenic?

PRRT2 p.Pro144= (c.432C>T) is classified Likely benign in PRRT2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-10-28). Ultra-rare (popmax 0.01%, amr); Associated with Inborn genetic diseases.

What condition is associated with PRRT2 p.Pro144= (c.432C>T)?

PRRT2 p.Pro144= (c.432C>T) is associated with Inborn genetic diseases, episodic kinesigenic dyskinesia (ClinVar).

How common is PRRT2 p.Pro144= (c.432C>T) in the general population?

PRRT2 p.Pro144= (c.432C>T) is ultra-rare (popmax 0.01%, amr) (gnomAD).

PRRT2 p.Pro144=

c.432C>T · rs749031499 · VCV536494

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.01%, amr)

Conditions

Inborn genetic diseases

⚠ 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 0.62	GERP -2.1, phastCons 0.73
Overall
CADD	5.584	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.01% Admixed American · 6/59,996 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.000868% 14/1,613,692 alleles · ultra-rare exomes 10/1,461,508 · genomes 4/152,184 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.01%	9,999
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,795
African / African-American	0.004%	24,971
European (non-Finnish)	0.000254%	393,255

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.Pro144=
Coding: c.432C>T
MANE Select: NM_145239
dbSNP: rs749031499
Type: single nucleotide variant
Location: chr16:29813486 (GRCh38)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: episodic kinesigenic dyskinesia

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-pro144 (accessed [today's date]).

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