LOX p.Pro174=
c.522C>T · rs764844537 · VCV2989875
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 0.47 | GERP -1.2, phastCons 0.99 |
| Overall | ||
| CADD | 10.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,038 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000186%
3/1,614,100 alleles · very rare
exomes 3/1,461,746 · genomes 0/152,354 · joint denominator
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.Pro174=
- Coding
- c.522C>T
- MANE Select
- NM_002317
- dbSNP
- rs764844537
- Type
- single nucleotide variant
- Location
- chr5:122077464 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 68.06
- Residue 174
- the 'disordered' region
Similar variants
- LOX p.Pro174His Uncertain significance ★★ ⚠ same residue
- LOX p.Pro174Thr Uncertain significance ★ ⚠ same residue
- 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
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-pro174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown