PLCB3 p.Glu60=
c.180G>A · rs149231506 · VCV712100
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.14%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.7 | GERP 0.72, phastCons 1 |
| Overall | ||
| CADD | 14.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.14%
South Asian · 1,950/91,022 alleles
Filtering AF
2.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.03%
Overall
0.158%
2,553/1,612,852 alleles · low-frequency
exomes 2,315/1,460,508 · genomes 238/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.14% | 47 |
| East Asian | 0.633% | 158 |
| Remaining individualsnot grpmax-eligible | 0.203% | 492 |
| Middle Eastern | 0.199% | 502 |
| African / African-American | 0.132% | 758 |
| Admixed American | 0.0217% | 4,617 |
| European (non-Finnish) | 0.00585% | 17,099 |
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.Glu60=
- Coding
- c.180G>A
- MANE Select
- NM_000932
- dbSNP
- rs149231506
- Type
- single nucleotide variant
- Location
- chr11:64254750 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 83.47 · 13 PDB
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.Pro171= Benign ★★ same type
- PLCB3 p.Ser845Leu Benign ★★ same type
- PLCB3 p.Thr158Met Likely benign ★★ same type
- PLCB3 p.Val806Ile Benign/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-glu60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown