PLCB3 p.Ala156=
c.468A>G · VCV4568899
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, afr)
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 -1.2 | GERP -3.4 |
| Overall | ||
| CADD | 5.578 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/74,912 alleles
Filtering AF
0.00816%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.000682%
11/1,613,980 alleles · ultra-rare
exomes 3/1,461,832 · genomes 8/152,148 · 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
- PLCB3
- Protein
- p.Ala156=
- Coding
- c.468A>G
- MANE Select
- NM_000932
- Type
- single nucleotide variant
- Location
- chr11:64255396 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.47 · 13 PDB
- Residue 156
- an α-helix
Similar variants
- PLCB3 p.Ser1107Leu Uncertain significance ★★ ⚠ same type
- PLCB3 c.2038+7C>A Benign ★★ same type
- PLCB3 c.99+8C>T Benign ★★ same type
- PLCB3 p.Glu1023Asp Benign ★★ same type
- PLCB3 p.Glu60= Benign ★★ same type
- PLCB3 p.Pro171= Benign ★★ same type
- PLCB3 p.Ser845Leu Benign ★★ same type
- PLCB3 p.Thr158Met Likely benign ★★ 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/plcb3-p-ala156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown