PLCB1 p.Phe570=
c.1710C>T · rs772233698 · VCV1542097
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.43 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.22 | loss · gain 0.01 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.3 | GERP -5.3 |
| Overall | ||
| CADD | 7.949 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,056 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0126%
Overall
0.00181%
29/1,604,946 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,028 |
| Admixed American | 0.0253% | 3,960 |
| East Asian | 0.00893% | 11,199 |
| Remaining individualsnot grpmax-eligible | 0.00483% | 20,706 |
| European (non-Finnish) | 0.000426% | 234,656 |
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
- PLCB1
- Protein
- p.Phe570=
- Coding
- c.1710C>T
- MANE Select
- NM_015192
- dbSNP
- rs772233698
- Type
- single nucleotide variant
- Location
- chr20:8727340 (GRCh38)
- Gene constraint
- LOEUF 0.357 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.55
- Residue 570
- the pi-plc y-box domain
Similar variants
- PLCB1 p.Arg222Ter Pathogenic/Likely pathogenic ★★ same condition
- PLCB1 p.Arg815Ter Pathogenic/Likely pathogenic ★★ same condition
- PLCB1 c.3336+3A>G Uncertain significance ★★ same condition
- PLCB1 p.Ala1046Ser Uncertain significance ★★ ⚠ same condition
- PLCB1 p.Ala1046Thr Uncertain significance ★★ ⚠ same condition
- PLCB1 p.Ala1116Val Uncertain significance ★★ ⚠ same condition
- PLCB1 p.Ala1182Val Uncertain significance ★★ ⚠ same condition
- PLCB1 p.Ala155Val Uncertain significance ★★ ⚠ same condition
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/plcb1-p-phe570 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown