PLD1 p.Val889=
c.2667A>C · rs9881788 · VCV1179602
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 68.8%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
cardiac valvular defect, developmental
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 3 | GERP -0.051, phastCons 1 |
| Overall | ||
| CADD | 2.792 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
68.8%
African / African-American · 51,285/74,544 alleles
Filtering AF
68.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 68.1%
Overall
44.9%
716,600/1,594,620 alleles · common
exomes 639,261/1,442,800 · genomes 77,339/151,820 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 68.8% | 1 |
| Finnishnot grpmax-eligible | 54.2% | 2 |
| Amishnot grpmax-eligible | 47.6% | 2 |
| Admixed American | 46.5% | 2 |
| European (non-Finnish) | 44.3% | 2 |
| Remaining individualsnot grpmax-eligible | 42.8% | 2 |
| East Asian | 38.2% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 35.3% | 3 |
| South Asian | 34.5% | 3 |
| Middle Eastern | 34.1% | 3 |
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
- PLD1
- Protein
- p.Val889=
- Coding
- c.2667A>C
- MANE Select
- NM_002662
- dbSNP
- rs9881788
- Type
- single nucleotide variant
- Location
- chr3:171620447 (GRCh38)
- Gene constraint
- LOEUF 0.822 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.92 · 2 PDB
- Residue 889
- the 'catalytic' region; a β-strand
Similar variants
- PLD1 c.2593+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PLD1 p.Arg407Ter Pathogenic/Likely pathogenic ★★ same condition
- PLD1 p.Arg298Gln Uncertain significance ★★ ⚠ same condition
- PLD1 p.Arg440His Uncertain significance ★★ ⚠ same condition
- PLD1 p.Asp661Val Uncertain significance ★★ ⚠ same condition
- PLD1 p.Gly834Ser Uncertain significance ★★ ⚠ same condition
- PLD1 p.Tyr894Cys Uncertain significance ★★ ⚠ same condition
- PLD1 p.Ala622Ser Benign ★★ 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/pld1-p-val889 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown