PLD1 p.Arg628=
c.1884T>C · rs2124147 · VCV1276405
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 68.5%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.012 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.37 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 8.061 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
68.5%
African / African-American · 51,312/74,914 alleles
Filtering AF
68%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 67.8%
Overall
45.1%
728,012/1,612,886 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 68.5% | 1 |
| Finnishnot grpmax-eligible | 54% | 2 |
| Amishnot grpmax-eligible | 47.8% | 2 |
| Admixed American | 46.3% | 2 |
| European (non-Finnish) | 44.8% | 2 |
| Remaining individualsnot grpmax-eligible | 42.9% | 2 |
| South Asian | 35% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 34.7% | 3 |
| East Asian | 34.3% | 3 |
| Middle Eastern | 33.7% | 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.Arg628=
- Coding
- c.1884T>C
- MANE Select
- NM_002662
- dbSNP
- rs2124147
- Type
- single nucleotide variant
- Location
- chr3:171677678 (GRCh38)
- Gene constraint
- LOEUF 0.822 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.92 · 2 PDB
- Residue 628
- the 'catalytic' region
Similar variants
- PLD1 p.Arg628Cys Uncertain significance ★ ⚠ same residue
- PLD1 p.Arg628His Uncertain significance ★ same residue
- PLD1 c.2430-1G>A Pathogenic/Likely pathogenic ★★ same type
- PLD1 c.2593+1G>A Pathogenic/Likely pathogenic ★★ same type
- PLD1 p.Arg407Ter Pathogenic/Likely pathogenic ★★ same type
- PLD1 p.Tyr894Ser Likely pathogenic ★★ same type
- PLD1 p.Ala689Val Uncertain significance ★★ ⚠ same type
- PLD1 p.Ala765Thr 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/pld1-p-arg628 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown