PLOD2 p.Arg724=
c.2170C>A · VCV3615017
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.57 | GERP -4.1, phastCons 0.18 |
| Overall | ||
| CADD | 5.163 | 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.Arg724=
- Coding
- c.2170C>A
- MANE Select
- NM_182943
- Type
- single nucleotide variant
- Location
- chr3:146070824 (GRCh38)
- Gene constraint
- LOEUF 1.209 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.63
- Residue 724
- the fe2og dioxygenase domain; a UniProt-annotated variant site (in brks2; likely pathogenic)
Similar variants
- PLOD2 p.Arg724Ter Uncertain significance ★★ same residue
- PLOD2 c.1500+1G>T Pathogenic/Likely pathogenic ★★ same type
- PLOD2 p.Arg440Ter Pathogenic/Likely pathogenic ★★ same type
- PLOD2 p.Arg473Ter Pathogenic ★★ same type
- PLOD2 p.Arg495Ter Pathogenic/Likely pathogenic ★★ same type
- PLOD2 p.Arg680Ter Pathogenic/Likely pathogenic ★★ same type
- PLOD2 c.1232+5T>A Uncertain significance ★★ same type
- PLOD2 c.-170C>G 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/plod2-p-arg724 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown