PCDH19 p.Pro256=
c.768C>T · rs761277974 · VCV1176317
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0141%, sas)
Conditions
1
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 -11 | GERP -5.5 |
| Overall | ||
| CADD | 0.635 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0141%
South Asian · 8/56,900 alleles
Filtering AF
0.00693%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00505%
Overall
0.000661%
8/1,211,094 alleles · ultra-rare
exomes 7/1,098,166 · genomes 1/112,928 · 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.Pro256=
- Coding
- c.768C>T
- MANE Select
- NM_001184880
- dbSNP
- rs761277974
- Type
- single nucleotide variant
- Location
- chrX:100407830 (GRCh38)
- Structure
- AlphaFold pLDDT 68.50 · 1 PDB
- Residue 256
- a UniProt-annotated variant site (in dee9); a β-strand; the cadherin 3 domain
Similar variants
- PCDH19 p.Pro256Ser 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
- PCDH19 p.Arg395Ter Pathogenic ★★ same condition
- PCDH19 p.Arg602Ter 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-pro256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown