PAX3

Chr 2

paired box 3

Also known as: CDHS, HUP2, PAX-3, WS1, WS3

NCBI Gene: 5077ENSG00000135903UniProt: P23760

This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. Mutations in paired box gene 3 are associated with Waardenburg syndrome, craniofacial-deafness-hand syndrome, and alveolar rhabdomyosarcoma. The translocation t(2;13)(q35;q14), which represents a fusion between PAX3 and the forkhead gene, is a frequent finding in alveolar rhabdomyosarcoma. Alternative splicing results in transcripts encoding isoforms with different C-termini. [provided by RefSeq, Jul 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtWaardenburg syndrome 1
UniProtWaardenburg syndrome 3
UniProtCraniofacial-deafness-hand syndrome
UniProtRhabdomyosarcoma 2

Clinical highlights

Gene-disease validity (ClinGen)
Waardenburg syndrome · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
2
Active trials
150
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.47
LOEUF
LOF*
Mechanism· G2P
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GeneReview available — PAX3
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.47LOEUF
pLI 0.241
Z-score 3.51
OE 0.24 (0.13–0.47)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.62Z-score
OE missense 0.73 (0.65–0.82)
206 obs / 282.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.24 (0.13–0.47)
0≤0.351.4
Missense OE?0.73 (0.65–0.82)
0≤0.61.4
Synonymous OE?1.08
0≤1.21.6
LoF obs/exp: 6 / 24.9Missense obs/exp: 206 / 282.5Syn Z: -0.68

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PAX3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients