PLD3 p.Ser183=
c.549C>T · rs371987481 · VCV1914377
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00239%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.8 | GERP -5.1 |
| Overall | ||
| CADD | 2.925 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00239%
East Asian · 1/41,902 alleles
Filtering AF
0.000628%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000484%
Overall
0.00102%
16/1,563,780 alleles · very rare
exomes 15/1,411,430 · genomes 1/152,350 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00239% | 41,902 |
| South Asian | 0.00234% | 42,810 |
| European (non-Finnish) | 0.00113% | 88,827 |
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
- PLD3
- Protein
- p.Ser183=
- Coding
- c.549C>T
- MANE Select
- NM_012268
- dbSNP
- rs371987481
- Type
- single nucleotide variant
- Location
- chr19:40370027 (GRCh38)
- Gene constraint
- LOEUF 0.727 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.15 · 7 PDB
- Residue 183
- an α-helix
Similar variants
- PLD3 p.Ala114Val Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg375Trp Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg413His Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg424Ser Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg457Gln Uncertain significance ★★ ⚠ same type
- PLD3 p.Arg488His Uncertain significance ★★ ⚠ same type
- PLD3 p.Asn313Asp Uncertain significance ★★ ⚠ same type
- PLD3 p.Gln137Arg 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/pld3-p-ser183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown