Is PCDH19 p.Ser893= (c.2679C>T) pathogenic?

PCDH19 p.Ser893= (c.2679C>T) is classified Likely benign in PCDH19 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-06). Absent from gnomAD v4.1; Associated with developmental and epileptic encephalopathy, 9.

What condition is associated with PCDH19 p.Ser893= (c.2679C>T)?

PCDH19 p.Ser893= (c.2679C>T) is associated with developmental and epileptic encephalopathy, 9 (ClinVar).

How common is PCDH19 p.Ser893= (c.2679C>T) in the general population?

PCDH19 p.Ser893= (c.2679C>T) is absent from gnomAD v4.1 (gnomAD).

PCDH19 p.Ser893=

c.2679C>T · VCV4704030

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 6.5	GERP 0.99, phastCons 1
Overall
CADD	9.836	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.Ser893=
Coding: c.2679C>T
MANE Select: NM_001184880
Type: single nucleotide variant
Location: chrX:100342072 (GRCh38)
Structure: AlphaFold pLDDT 68.50 · 1 PDB
Residue 893: a UniProt-annotated variant site (in dee9)

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 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
PCDH19 p.Arg602Ter Pathogenic ★★ same condition
PCDH19 p.Arg886Ter 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-ser893 (accessed [today's date]).

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