Is PCDH19 p.Pro55= (c.165C>G) pathogenic?

PCDH19 p.Pro55= (c.165C>G) is classified Likely benign in PCDH19 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-12-17). Absent from gnomAD v4.1; Associated with developmental and epileptic encephalopathy, 9.

What condition is associated with PCDH19 p.Pro55= (c.165C>G)?

PCDH19 p.Pro55= (c.165C>G) is associated with developmental and epileptic encephalopathy, 9 (ClinVar).

How common is PCDH19 p.Pro55= (c.165C>G) in the general population?

PCDH19 p.Pro55= (c.165C>G) is absent from gnomAD v4.1 (gnomAD).

PCDH19 p.Pro55=

c.165C>G · rs1002430549 · VCV415288

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.47	GERP -5.5, phastCons 0.003
Overall
CADD	4.874	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PCDH19
Protein: p.Pro55=
Coding: c.165C>G
MANE Select: NM_001184880
dbSNP: rs1002430549
Type: single nucleotide variant
Location: chrX:100408433 (GRCh38)
Structure: AlphaFold pLDDT 68.50 · 1 PDB
Residue 55: the cadherin 1 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.Pro55Arg Uncertain significance ★ ⚠ same residue
PCDH19 p.Pro55Ser Conflicting classifications of pathogenicity ★ ⚠ 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
PCDH19 p.Arg395Ter 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-pro55 (accessed [today's date]).

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