PLCE1 p.Ser1190=
c.3570T>C · VCV4709392
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.30 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP -0.58, phastCons 1 |
| Overall | ||
| CADD | 11.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,856 alleles
Overall
6.2e-05%
1/1,614,092 alleles · very rare
exomes 1/1,461,772 · genomes 0/152,320 · 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
- PLCE1
- Protein
- p.Ser1190=
- Coding
- c.3570T>C
- MANE Select
- NM_016341
- Type
- single nucleotide variant
- Location
- chr10:94258815 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.01 · 3 PDB
- Residue 1190
- a UniProt-annotated variant site (in nphs3); the 'disordered' region
Similar variants
- PLCE1 p.Ser1190Gly Uncertain significance ★★ ⚠ same residue
- PLCE1 c.4506+1G>A Likely pathogenic ★★ same type
- PLCE1 c.6132+1G>A Likely pathogenic ★★ same type
- PLCE1 p.Arg1246Ter Pathogenic ★★ same type
- PLCE1 p.Arg1434Gln Likely pathogenic ★★ same type
- PLCE1 p.Arg1495Ter Pathogenic/Likely pathogenic ★★ same type
- PLCE1 p.Arg321Ter Pathogenic ★★ same type
- PLCE1 p.Arg493Ter Pathogenic ★★ same type
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/plce1-p-ser1190 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown