PAX5

Chr 9

paired box 5

Also known as: ALL3, BSAP, PAX-5

This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. Paired box transcription factors are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. This gene encodes the B-cell lineage specific activator protein that is expressed at early, but not late stages of B-cell differentiation. Its expression has also been detected in developing CNS and testis and so the encoded protein may also play a role in neural development and spermatogenesis. This gene is located at 9p13, which is involved in t(9;14)(p13;q32) translocations recurring in small lymphocytic lymphomas of the plasmacytoid subtype, and in derived large-cell lymphomas. This translocation brings the potent E-mu enhancer of the IgH gene into close proximity of the PAX5 promoter, suggesting that the deregulation of transcription of this gene contributes to the pathogenesis of these lymphomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

OMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

{Leukemia, acute lymphoblastic, susceptibility to, 3}MIM #615545

Clinical highlights

Gene-disease validity (ClinGen)
PAX5-related B lymphopenia and autism spectrum disorder · ARModerateconsider for supplementary testing2 gene-disease associations curated in total
Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
223
Pubs (1 yr)
P/LP submissions
P/LP missense
0.17
LOEUF· LoF intol.
Multiple*
Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint?
0.17LOEUF
pLI 0.998
Z-score 3.95
OE 0.00 (0.000.17)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
2.45Z-score
OE missense 0.56 (0.490.65)
139 obs / 247.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.00 (0.000.17)
00.351.4
Missense OE?0.56 (0.490.65)
00.61.4
Synonymous OE?1.06
01.21.6
LoF obs/exp: 0 / 18.1Missense obs/exp: 139 / 247.6Syn Z: -0.47

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

PAX5 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →