PLCB3 p.Pro171=
c.513C>T · rs143887717 · VCV712101
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.36%, 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 -3.4 |
| Overall | ||
| CADD | 0.749 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.36%
South Asian · 2,150/91,084 alleles
Filtering AF
2.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.24%
Overall
0.175%
2,829/1,614,130 alleles · low-frequency
exomes 2,579/1,461,830 · genomes 250/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.36% | 42 |
| East Asian | 0.637% | 157 |
| Remaining individualsnot grpmax-eligible | 0.218% | 460 |
| Middle Eastern | 0.181% | 551 |
| African / African-American | 0.133% | 750 |
| Admixed American | 0.0233% | 4,287 |
| European (non-Finnish) | 0.0111% | 9,008 |
| Finnishnot grpmax-eligible | 0.00156% | 64,004 |
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.Pro171=
- Coding
- c.513C>T
- MANE Select
- NM_000932
- dbSNP
- rs143887717
- Type
- single nucleotide variant
- Location
- chr11:64255441 (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.Glu60= 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-pro171 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown