PLOD2 p.Val702=
c.2106G>C · rs147997412 · VCV712702
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.939%, afr)
Conditions
2
Bruck syndrome 2
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 0.41 | GERP -2.1, phastCons 0.99 |
| Overall | ||
| CADD | 3.391 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.939%
African / African-American · 702/74,750 alleles
Filtering AF
0.882%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.859%
Overall
0.0492%
791/1,607,792 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.939% | 106 |
| Remaining individualsnot grpmax-eligible | 0.0659% | 1,518 |
| Admixed American | 0.0637% | 1,571 |
| Middle Eastern | 0.0331% | 3,017 |
| South Asian | 0.00551% | 18,160 |
| European (non-Finnish) | 0.000255% | 391,764 |
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
- PLOD2
- Protein
- p.Val702=
- Coding
- c.2106G>C
- MANE Select
- NM_182943
- dbSNP
- rs147997412
- Type
- single nucleotide variant
- Location
- chr3:146071057 (GRCh38)
- Gene constraint
- LOEUF 1.209 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.63
- Residue 702
- the fe2og dioxygenase domain; a UniProt-annotated variant site (in brks2; likely pathogenic)
Similar variants
- PLOD2 p.Val702Leu Uncertain significance ★★ ⚠ same residue
- PLOD2 p.Val702Met Uncertain significance ★ ⚠ same residue
- 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.Arg484Cys 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-val702 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown