PLD2 p.Arg336=
c.1008G>A · rs147917834 · VCV732827
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.126%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | donor loss, 1 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 13.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.126%
European (non-Finnish) · 1,486/1,178,848 alleles
Filtering AF
0.121%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.118%
Overall
0.0995%
1,600/1,608,582 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.126% | 793 |
| Remaining individualsnot grpmax-eligible | 0.0545% | 1,835 |
| Finnishnot grpmax-eligible | 0.0378% | 2,644 |
| South Asian | 0.0363% | 2,752 |
| African / African-American | 0.024% | 4,159 |
| Admixed American | 0.0101% | 9,935 |
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
- PLD2
- Protein
- p.Arg336=
- Coding
- c.1008G>A
- MANE Select
- NM_002663
- dbSNP
- rs147917834
- Type
- single nucleotide variant
- Location
- chr17:4810949 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.55 · 6 PDB
- Residue 336
- a β-strand
Similar variants
- PLD2 p.Arg336Gln Uncertain significance ★ ⚠ same residue
- PLD2 p.Arg336Pro Uncertain significance ★ ⚠ same residue
- PLD2 p.Arg336Trp Uncertain significance ★ ⚠ same residue
- PLD2 c.2010-9C>T Benign ★★ same type
- PLD2 p.Arg330Gln Benign ★★ ⚠ same type
- PLD2 p.Arg490Cys Likely benign ★★ same type
- PLD2 p.Arg553Gln Benign ★★ ⚠ same type
- PLD2 p.His278Tyr Benign ★★ 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/pld2-p-arg336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown