PLCB1 p.Val1045=
c.3135C>T · rs577076166 · VCV196139
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, 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 -1.6 | GERP -3.2 |
| Overall | ||
| CADD | 5.572 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,916 alleles
Filtering AF
0.00544%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00136%
22/1,613,448 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,559 |
| East Asian | 0.00669% | 14,942 |
| South Asian | 0.0022% | 45,459 |
| European (non-Finnish) | 0.000848% | 117,984 |
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.Val1045=
- Coding
- c.3135C>T
- MANE Select
- NM_015192
- dbSNP
- rs577076166
- Type
- single nucleotide variant
- Location
- chr20:8788472 (GRCh38)
- Gene constraint
- LOEUF 0.357 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.55
Similar variants
- PLCB1 p.Val1045Ile Uncertain significance ★ ⚠ same residue
- 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
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-val1045 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown