PLCB4 p.Ile501=
c.1503C>T · rs753456784 · VCV2796905
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.153%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -4.5, phastCons 1 |
| Overall | ||
| CADD | 12.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.153%
Admixed American · 92/59,952 alleles
Filtering AF
0.128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.119%
Overall
0.00643%
103/1,601,464 alleles · rare
exomes 88/1,449,310 · genomes 15/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.153% | 652 |
| Remaining individualsnot grpmax-eligible | 0.00483% | 20,689 |
| Finnishnot grpmax-eligible | 0.00157% | 63,526 |
| European (non-Finnish) | 0.000599% | 167,024 |
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
- PLCB4
- Protein
- p.Ile501=
- Coding
- c.1503C>T
- MANE Select
- NM_001377142
- dbSNP
- rs753456784
- Type
- single nucleotide variant
- Location
- chr20:9395611 (GRCh38)
- Gene constraint
- LOEUF 0.509 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 86.03
- Residue 501
- the 'disordered' region
Similar variants
- PLCB4 p.Ile501Thr Uncertain significance ★ ⚠ same residue
- PLCB4 p.Arg633Cys Pathogenic ★★ same type
- PLCB4 p.Arg633His Pathogenic ★★ same type
- PLCB4 p.Asp642Asn Pathogenic/Likely pathogenic ★★ same type
- PLCB4 c.1323+8T>C Uncertain significance ★★ same type
- PLCB4 c.*586C>T Uncertain significance ★★ same type
- PLCB4 p.Arg640Gln Uncertain significance ★★ ⚠ same type
- PLCB4 p.Glu1005Lys Uncertain significance ★★ ⚠ 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/plcb4-p-ile501 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown