PLCB3 p.Asn686=
c.2058C>T · VCV4821283
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
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 -13 | GERP -4 |
| Overall | ||
| CADD | 1.834 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,086 alleles
Filtering AF
0.00111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0009%
Overall
0.00161%
26/1,613,574 alleles · very rare
exomes 23/1,461,198 · genomes 3/152,376 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,362 |
| East Asian | 0.00223% | 44,876 |
| European (non-Finnish) | 0.0017% | 58,989 |
| Admixed American | 0.00167% | 60,028 |
| African / African-American | 0.00133% | 75,066 |
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.Asn686=
- Coding
- c.2058C>T
- MANE Select
- NM_000932
- Type
- single nucleotide variant
- Location
- chr11:64262426 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.47 · 13 PDB
- Residue 686
- an α-helix; 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-asn686 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown