PLCB3 p.Ser618=
c.1854G>A · VCV3889952
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.396%, mid)
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 -9.1 | GERP -4 |
| Overall | ||
| CADD | 2.249 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.396%
Middle Eastern · 24/6,062 alleles
Filtering AF
0.273%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.232%
Overall
0.00564%
91/1,614,128 alleles · rare
exomes 85/1,461,834 · genomes 6/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.396% | 253 |
| Admixed American | 0.0183% | 5,456 |
| South Asian | 0.0165% | 6,072 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| European (non-Finnish) | 0.00271% | 36,875 |
| African / African-American | 0.00133% | 75,036 |
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.Ser618=
- Coding
- c.1854G>A
- MANE Select
- NM_000932
- Type
- single nucleotide variant
- Location
- chr11:64261606 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.47 · 13 PDB
- Residue 618
- a β-strand; the pi-plc y-box domain
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-ser618 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown