LOX p.Cys412=
c.1236C>T · rs2532900813 · VCV1756950
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.51e-05%, nfe)
Conditions
1
Cardiovascular phenotype
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 5.1 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 12.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.51e-05%
European (non-Finnish) · 1/1,175,570 alleles
Overall
6.86e-05%
1/1,456,760 alleles · very rare
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
- LOX
- Protein
- p.Cys412=
- Coding
- c.1236C>T
- MANE Select
- NM_002317
- dbSNP
- rs2532900813
- Type
- single nucleotide variant
- Location
- chr5:122070064 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 68.06
- Residue 412
- a disulfide bond; the 'lysyl-oxidase like' region
Similar variants
- LOX p.Arg281Ter Pathogenic/Likely pathogenic ★★ same condition
- LOX p.Gly202Ter Pathogenic/Likely pathogenic ★★ same condition
- LOX c.1247+1G>A Uncertain significance ★★ same condition
- LOX p.Ala100Thr Uncertain significance ★★ ⚠ same condition
- LOX p.Ala107Thr Uncertain significance ★★ ⚠ same condition
- LOX p.Ala147Thr Uncertain significance ★★ ⚠ same condition
- LOX p.Arg162Cys Uncertain significance ★★ ⚠ same condition
- LOX p.Arg281Gln 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/lox-p-cys412 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown