Is LOX p.Pro35= (c.105G>T) pathogenic?

LOX p.Pro35= (c.105G>T) is classified Likely benign in LOX (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-11). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with LOX p.Pro35= (c.105G>T)?

LOX p.Pro35= (c.105G>T) is associated with Cardiovascular phenotype (ClinVar).

How common is LOX p.Pro35= (c.105G>T) in the general population?

LOX p.Pro35= (c.105G>T) is absent from gnomAD v4.1 (gnomAD).

LOX p.Pro35=

c.105G>T · rs1363519852 · VCV1780000

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,534,800)

Conditions

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 -2.4	GERP -2.7
Overall
CADD	6.485	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,534,800). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: LOX
Protein: p.Pro35=
Coding: c.105G>T
MANE Select: NM_002317
dbSNP: rs1363519852
Type: single nucleotide variant
Location: chr5:122077881 (GRCh38)
Gene constraint: LOEUF 0.503 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 68.06

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

Similar variants

LOX p.Pro35Gln Conflicting classifications of pathogenicity ★ ⚠ 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
LOX p.Arg162Cys 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-pro35 (accessed [today's date]).

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