PLOD2 p.Lys665=
c.1995G>A · rs1936119443 · VCV900157
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Bruck syndrome 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.55 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.76 | loss · gain 0.49 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 24.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PLOD2
- Protein
- p.Lys665=
- Coding
- c.1995G>A
- MANE Select
- NM_182943
- dbSNP
- rs1936119443
- Type
- single nucleotide variant
- Location
- chr3:146071277 (GRCh38)
- Gene constraint
- LOEUF 1.209 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.63
- Residue 665
- the fe2og dioxygenase domain; a UniProt-annotated variant site (in brks2; likely pathogenic)
Similar variants
- PLOD2 p.Arg440Ter Pathogenic/Likely pathogenic ★★ same condition
- PLOD2 p.Arg495Ter Pathogenic/Likely pathogenic ★★ same condition
- PLOD2 p.Arg680Ter Pathogenic/Likely pathogenic ★★ same condition
- PLOD2 c.-170C>G Uncertain significance ★★ same condition
- PLOD2 p.Ala415Val Uncertain significance ★★ ⚠ same condition
- PLOD2 p.Arg619Cys Uncertain significance ★★ ⚠ same condition
- PLOD2 p.Arg648Trp Uncertain significance ★★ ⚠ same condition
- PLOD2 p.Asp102Glu Uncertain significance ★★ ⚠ 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/plod2-p-lys665 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown