LOX p.Arg70=
c.210G>A · rs1365060314 · VCV2965230
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0169%, mid)
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 0.18 | GERP -3.5, phastCons 0.9 |
| Overall | ||
| CADD | 8.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0169%
Middle Eastern · 1/5,914 alleles
Filtering AF
0.00154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000828%
Overall
0.000358%
5/1,397,102 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0169% | 5,914 |
| Admixed American | 0.00582% | 17,168 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,254 |
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.Arg70=
- Coding
- c.210G>A
- MANE Select
- NM_002317
- dbSNP
- rs1365060314
- Type
- single nucleotide variant
- Location
- chr5:122077776 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 68.06
- Residue 70
- the 'disordered' region
Similar variants
- LOX p.Arg70Gln Uncertain significance ★ ⚠ same residue
- LOX p.Arg70Trp Uncertain significance ★★ ⚠ same residue
- 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
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-arg70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown