PLD1 p.Ser455=
c.1365A>G · rs139677913 · VCV791960
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.49%, afr)
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 -20 | GERP -4.5 |
| Overall | ||
| CADD | 0.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.49%
African / African-American · 1,119/75,010 alleles
Filtering AF
1.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.39%
Overall
0.0773%
1,248/1,613,988 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.49% | 67 |
| Middle Eastern | 0.132% | 757 |
| Remaining individualsnot grpmax-eligible | 0.104% | 962 |
| Admixed American | 0.085% | 1,177 |
| South Asian | 0.0011% | 91,072 |
| European (non-Finnish) | 0.000339% | 294,982 |
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.Ser455=
- Coding
- c.1365A>G
- MANE Select
- NM_002662
- dbSNP
- rs139677913
- Type
- single nucleotide variant
- Location
- chr3:171688850 (GRCh38)
- Gene constraint
- LOEUF 0.822 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.92 · 2 PDB
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-ser455 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown