PLD1 p.Leu262=
c.786A>G · rs1717470740 · VCV2963398
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.33 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.6 | phastCons 0.002 |
| Overall | ||
| CADD | 6.654 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,834 alleles
Overall
0.000124%
2/1,606,754 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,834 |
| European (non-Finnish) | 8.52e-05% | 1,173,796 |
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.Leu262=
- Coding
- c.786A>G
- MANE Select
- NM_002662
- dbSNP
- rs1717470740
- Type
- single nucleotide variant
- Location
- chr3:171714018 (GRCh38)
- Gene constraint
- LOEUF 0.822 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.92 · 2 PDB
- Residue 262
- 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-leu262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown