PLCE1 p.Asp784=
c.2352C>T · rs201793869 · VCV301704
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.29%, sas)
Conditions
2
kidney disorder
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 0.62 | GERP -3.9, phastCons 0.99 |
| Overall | ||
| CADD | 10.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.29%
South Asian · 2,083/91,060 alleles
Filtering AF
2.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.17%
Overall
0.145%
2,348/1,613,990 alleles · low-frequency
exomes 2,159/1,461,766 · genomes 189/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.29% | 44 |
| Middle Eastern | 0.363% | 276 |
| Remaining individualsnot grpmax-eligible | 0.141% | 710 |
| Admixed American | 0.07% | 1,429 |
| African / African-American | 0.0626% | 1,596 |
| East Asian | 0.0111% | 8,974 |
| European (non-Finnish) | 0.00517% | 19,344 |
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
- PLCE1
- Protein
- p.Asp784=
- Coding
- c.2352C>T
- MANE Select
- NM_016341
- dbSNP
- rs201793869
- Type
- single nucleotide variant
- Location
- chr10:94236052 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.01 · 3 PDB
- Residue 784
- the ras-gef domain
Similar variants
- PLCE1 c.4506+1G>A Likely pathogenic ★★ same condition
- PLCE1 c.6132+1G>A Likely pathogenic ★★ same condition
- PLCE1 p.Arg1246Ter Pathogenic ★★ same condition
- PLCE1 p.Arg1434Gln Likely pathogenic ★★ same condition
- PLCE1 p.Arg1495Ter Pathogenic/Likely pathogenic ★★ same condition
- PLCE1 p.Arg321Ter Pathogenic ★★ same condition
- PLCE1 p.Arg493Ter Pathogenic ★★ same condition
- PLCE1 p.Gln1020Ter Pathogenic ★★ 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/plce1-p-asp784 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown