Is PCDH19 p.Pro451= (c.1353G>T) pathogenic?

PCDH19 p.Pro451= (c.1353G>T) is classified Likely benign in PCDH19 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-14). Very rare (popmax 0.000112%, nfe); Associated with developmental and epileptic encephalopathy, 9.

What condition is associated with PCDH19 p.Pro451= (c.1353G>T)?

PCDH19 p.Pro451= (c.1353G>T) is associated with developmental and epileptic encephalopathy, 9 (ClinVar).

How common is PCDH19 p.Pro451= (c.1353G>T) in the general population?

PCDH19 p.Pro451= (c.1353G>T) is very rare (popmax 0.000112%, nfe) (gnomAD).

PCDH19 p.Pro451=

c.1353G>T · rs373795773 · VCV1529985

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

Conditions

developmental and epileptic encephalopathy, 9

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -12	GERP -5.5
Overall
CADD	0.125	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000112% European (non-Finnish) · 1/895,532 alleles

Overall 8.25e-05% 1/1,211,717 alleles · very rare exomes 1/1,098,221 · genomes 0/113,496 · 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: PCDH19
Protein: p.Pro451=
Coding: c.1353G>T
MANE Select: NM_001184880
dbSNP: rs373795773
Type: single nucleotide variant
Location: chrX:100407245 (GRCh38)
Structure: AlphaFold pLDDT 68.50 · 1 PDB
Residue 451: a UniProt-annotated variant site (in dee9); the cadherin 4 domain

Full PCDH19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental and epileptic encephalopathy, 9 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PCDH19 p.Pro451Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
PCDH19 p.Pro451Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
PCDH19 p.Pro451Thr Uncertain significance ★ ⚠ same residue
PCDH19 c.2675+1G>T Pathogenic/Likely pathogenic ★★ same condition
PCDH19 c.2675+2T>C Pathogenic ★★ same condition
PCDH19 p.Arg198Leu Pathogenic/Likely pathogenic ★★ same condition
PCDH19 p.Arg207Ter Pathogenic ★★ same condition
PCDH19 p.Arg372Trp Pathogenic/Likely 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/pcdh19-p-pro451 (accessed [today's date]).

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