PLCB1 p.Lys14=
c.42G>A · rs775655063 · VCV698239
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, amr)
Conditions
2
Inborn genetic diseases
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 5.4 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 13.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/59,952 alleles
Filtering AF
0.0128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0101%
Overall
0.00118%
19/1,612,914 alleles · ultra-rare
exomes 17/1,460,742 · genomes 2/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,612 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,408 |
| African / African-American | 0.00134% | 74,868 |
| European (non-Finnish) | 0.000339% | 294,850 |
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.Lys14=
- Coding
- c.42G>A
- MANE Select
- NM_015192
- dbSNP
- rs775655063
- Type
- single nucleotide variant
- Location
- chr20:8132693 (GRCh38)
- Gene constraint
- LOEUF 0.357 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.55
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-lys14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown