PCDH19 p.Ser239=
c.717C>T · rs199628956 · VCV138597
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.142%, afr)
Conditions
2
Inborn genetic diseases
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 -1.3 | GERP -5.5 |
| Overall | ||
| CADD | 5.036 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.142%
African / African-American · 82/57,681 alleles
Filtering AF
0.117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.108%
Overall
0.00883%
107/1,211,119 alleles · rare
exomes 52/1,097,873 · genomes 55/113,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.142% | 703 |
| Admixed American | 0.0369% | 2,710 |
| Middle Eastern | 0.023% | 4,356 |
| Remaining individualsnot grpmax-eligible | 0.0147% | 6,807 |
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.Ser239=
- Coding
- c.717C>T
- MANE Select
- NM_001184880
- dbSNP
- rs199628956
- Type
- single nucleotide variant
- Location
- chrX:100407881 (GRCh38)
- Structure
- AlphaFold pLDDT 68.50 · 1 PDB
- Residue 239
- a UniProt-annotated variant site (in dee9); a β-strand; the cadherin 3 domain
Similar variants
- PCDH19 p.Ser239Arg 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-ser239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown