PLD1 p.Val986=
c.2958G>C · VCV3667219
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
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 · C>T here scores Δ0.50 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -3.5 |
| Overall | ||
| CADD | 1.444 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/75,038 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000494%
Overall
0.000205%
3/1,461,424 alleles · very rare
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.Val986=
- Coding
- c.2958G>C
- MANE Select
- NM_002662
- Type
- single nucleotide variant
- Location
- chr3:171605341 (GRCh38)
- Gene constraint
- LOEUF 0.822 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.92 · 2 PDB
- Residue 986
- an α-helix
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-val986 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown