PLD1 p.Asp268=
c.804C>T · rs138256899 · VCV748143
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.26 | gain · loss 0.22 · SpliceAI calls loss · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.6 | phastCons 1 |
| Overall | ||
| CADD | 5.552 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
African / African-American · 14/74,838 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00905%
Overall
0.000933%
15/1,608,280 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0187% | 5,346 |
| European (non-Finnish) | 8.51e-05% | 1,174,811 |
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.Asp268=
- Coding
- c.804C>T
- MANE Select
- NM_002662
- dbSNP
- rs138256899
- Type
- single nucleotide variant
- Location
- chr3:171714000 (GRCh38)
- Gene constraint
- LOEUF 0.822 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.92 · 2 PDB
- Residue 268
- the ph domain
Similar variants
- 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
- PLD1 p.Arg172Lys Uncertain significance ★★ ⚠ same type
- PLD1 p.Arg298Gln 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-asp268 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown