Is PCDH19 p.Arg47= (c.139C>A) pathogenic?

PCDH19 p.Arg47= (c.139C>A) is classified Likely benign in PCDH19 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-05). No allele count reported in gnomAD v4.1 (AN 1,205,266); Associated with developmental and epileptic encephalopathy, 9.

What condition is associated with PCDH19 p.Arg47= (c.139C>A)?

PCDH19 p.Arg47= (c.139C>A) is associated with developmental and epileptic encephalopathy, 9 (ClinVar).

How common is PCDH19 p.Arg47= (c.139C>A) in the general population?

PCDH19 p.Arg47= (c.139C>A) is no allele count reported in gnomAD v4.1 (AN 1,205,266) (gnomAD).

PCDH19 p.Arg47=

c.139C>A · VCV4732587

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,205,266)

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 6.6	GERP 1.8, phastCons 1
Overall
CADD	11.14	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,205,266). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PCDH19
Protein: p.Arg47=
Coding: c.139C>A
MANE Select: NM_001184880
Type: single nucleotide variant
Location: chrX:100408459 (GRCh38)
Structure: AlphaFold pLDDT 68.50 · 1 PDB
Residue 47: an α-helix; 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.Arg47Leu Uncertain significance ★ ⚠ same residue
PCDH19 p.Arg47Ter Pathogenic ★ 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-arg47 (accessed [today's date]).

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