LOX p.Pro66=
c.198T>C · rs769991965 · VCV1783956
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00411%, afr)
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 -1.1 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 8.212 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00411%
African / African-American · 3/72,944 alleles
Filtering AF
0.00109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000503%
Overall
0.000194%
3/1,548,646 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.Pro66=
- Coding
- c.198T>C
- MANE Select
- NM_002317
- dbSNP
- rs769991965
- Type
- single nucleotide variant
- Location
- chr5:122077788 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 68.06
- Residue 66
- the 'disordered' 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-pro66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown