PLD3 p.Phe50=
c.150C>T · rs765220946 · VCV2196427
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0061%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.4 | GERP -4.8 |
| Overall | ||
| CADD | 8.179 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0061%
European (non-Finnish) · 72/1,179,916 alleles
Filtering AF
0.00495%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00455%
Overall
0.00458%
74/1,613,982 alleles · very rare
exomes 70/1,461,700 · genomes 4/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0061% | 16,388 |
| Admixed American | 0.00333% | 30,006 |
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.Phe50=
- Coding
- c.150C>T
- MANE Select
- NM_012268
- dbSNP
- rs765220946
- Type
- single nucleotide variant
- Location
- chr19:40366820 (GRCh38)
- Gene constraint
- LOEUF 0.727 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.15 · 7 PDB
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-phe50 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown