Is LOX p.Asp164= (c.492C>T) pathogenic?

LOX p.Asp164= (c.492C>T) is classified Likely benign in LOX (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-12). Very rare (popmax 0.00133%, afr); Associated with Cardiovascular phenotype.

What condition is associated with LOX p.Asp164= (c.492C>T)?

LOX p.Asp164= (c.492C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is LOX p.Asp164= (c.492C>T) in the general population?

LOX p.Asp164= (c.492C>T) is very rare (popmax 0.00133%, afr) (gnomAD).

LOX p.Asp164=

c.492C>T · rs904395934 · VCV1744175

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.61	GERP -3.2, phastCons 1
Overall
CADD	10.43	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,068 alleles

Overall 6.84e-05% 1/1,461,570 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.Asp164=
Coding: c.492C>T
MANE Select: NM_152546 · reported on NM_002317
dbSNP: rs904395934
Type: single nucleotide variant
Location: chr5:122077494 (GRCh38)

Full LOX gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-asp164 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown