PLD1 p.Val653=
c.1959C>T · rs765929750 · VCV3039085
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00602%, nfe)
Conditions
1
PLD1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.074 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 9.676 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00602%
European (non-Finnish) · 71/1,179,906 alleles
Filtering AF
0.00486%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00447%
Overall
0.00446%
72/1,613,896 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00602% | 16,618 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,476 |
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.Val653=
- Coding
- c.1959C>T
- MANE Select
- NM_002662
- dbSNP
- rs765929750
- Type
- single nucleotide variant
- Location
- chr3:171677603 (GRCh38)
- Gene constraint
- LOEUF 0.822 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.92 · 2 PDB
- Residue 653
- the 'catalytic' region
Disease context
PLD1-related disorder
Similar variants
- PLD1 p.Val653Ile Uncertain significance ★★ ⚠ same residue
- PLD1 p.Tyr894Ser Likely pathogenic ★★ same condition
- PLD1 p.Arg746Cys Uncertain significance ★★ ⚠ same condition
- PLD1 p.Glu129Lys Uncertain significance ★★ ⚠ same condition
- PLD1 p.Arg1032Ter Conflicting classifications of pathogenicity ★ same condition
- PLD1 p.Thr293= Likely benign same condition
- PLD1 p.Tyr433= Likely benign same condition
- PLD1 p.Ile805_Leu806insTer Pathogenic/Likely pathogenic ★★ same condition
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-val653 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown