PAX1
Chr 20ARpaired box 1
Also known as: HUP48, OFC2, OTFCS2
PAX1 encodes a transcription factor that activates gene expression and is essential for vertebral column development and formation of segmented embryonic structures. Mutations cause otofaciocervical syndrome 2 with T-cell deficiency, which involves vertebral malformations and immune deficiency, inherited in an autosomal recessive pattern. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.498), consistent with its critical developmental role.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Tolerant to missense variation
This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to loss-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
PAX1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Cervical Cytology DNA Methylation for Cervical Cancer Screening
NOT YET RECRUITINGPredicting Treatment Failure in HSIL Patients with Positive Margins After Conization Via Detection of PAX1 Methylation
NOT YET RECRUITINGExternal Resources
Links to major genomics databases and tools