PLD3 p.Pro17=
c.51C>T · rs200094590 · VCV2046284
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.965%, amr)
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 -5.1 | GERP -4.8 |
| Overall | ||
| CADD | 0.908 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.965%
Admixed American · 542/56,172 alleles
Filtering AF
0.898%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.871%
Overall
0.0361%
571/1,580,808 alleles · rare
exomes 412/1,428,554 · genomes 159/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.965% | 104 |
| Remaining individualsnot grpmax-eligible | 0.0246% | 4,063 |
| African / African-American | 0.00943% | 10,599 |
| East Asian | 0.00224% | 44,564 |
| European (non-Finnish) | 0.000516% | 193,640 |
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
- PLD3
- Protein
- p.Pro17=
- Coding
- c.51C>T
- MANE Select
- NM_012268
- dbSNP
- rs200094590
- Type
- single nucleotide variant
- Location
- chr19:40366633 (GRCh38)
- Gene constraint
- LOEUF 0.727 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.15 · 7 PDB
Similar variants
- PLD3 p.Pro17Leu Uncertain significance ★ ⚠ same residue
- PLD3 p.Ala114Val Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg375Trp Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg413His Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg424Ser Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg457Gln Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg488His Uncertain significance ★★ ⚠ same type
- PLD3 p.Asn313Asp 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/pld3-p-pro17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown