LOX p.Pro279=
c.837C>G · rs199714078 · VCV1926464
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -1.1 | GERP -3.9, phastCons 0.003 |
| Overall | ||
| CADD | 10.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,852 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000277%
Overall
0.000248%
4/1,613,768 alleles · very rare
exomes 2/1,461,514 · genomes 2/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,426 |
| South Asian | 0.0022% | 45,509 |
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.Pro279=
- Coding
- c.837C>G
- MANE Select
- NM_002317
- dbSNP
- rs199714078
- Type
- single nucleotide variant
- Location
- chr5:122075445 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 68.06
- Residue 279
- the 'lysyl-oxidase like' region
Similar variants
- LOX c.1035+1G>A Pathogenic/Likely pathogenic ★★ same type
- LOX c.740+1G>T Pathogenic/Likely pathogenic ★★ same type
- LOX p.Arg281Ter Pathogenic/Likely pathogenic ★★ same type
- LOX p.Gly202Ter Pathogenic/Likely pathogenic ★★ same type
- LOX p.Met298Arg Pathogenic/Likely pathogenic ★★ same type
- LOX p.Trp124Ter Pathogenic ★★ same type
- LOX p.Trp42Ter Pathogenic/Likely pathogenic ★★ same type
- LOX p.Tyr227Ter Pathogenic/Likely pathogenic ★★ 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/lox-p-pro279 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown