PAX5
Basic information
Region (hg38): 9:36833269-37034268
Links
Phenotypes
GenCC
Source:
- leukemia, acute lymphoblastic, susceptibility to, 3 (Limited), mode of inheritance: AD
- leukemia, acute lymphoblastic, susceptibility to, 3 (Moderate), mode of inheritance: AD
- PAX5-related B lymphopenia and autism spectrum disorder (Moderate), mode of inheritance: AR
- neurodevelopmental disorder (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Leukemia, acute lymphoblastic, susceptibility to, 3 | AD | Oncologic | Awareness of B-ALL risk may allow surveillance and early detection and management, which may benefit morbidity and mortality; HSCT has been described | Oncologic | 24013638 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (353 variants)
- not_provided (128 variants)
- not_specified (35 variants)
- Leukemia,_acute_lymphoblastic,_susceptibility_to,_3 (17 variants)
- Acute_lymphoid_leukemia (17 variants)
- PAX5-related_disorder (8 variants)
- Neurodevelopmental_disorder (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAX5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016734.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 181 | 182 | ||||
missense | 201 | 218 | ||||
nonsense | 6 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
Total | 3 | 17 | 205 | 186 | 3 |
Highest pathogenic variant AF is 0.00000822464
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PAX5 | protein_coding | protein_coding | ENST00000358127 | 10 | 200832 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.998 | 0.00202 | 125509 | 0 | 10 | 125519 | 0.0000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.45 | 139 | 248 | 0.561 | 0.0000151 | 2484 |
Missense in Polyphen | 39 | 108.85 | 0.35829 | 1066 | ||
Synonymous | -0.469 | 112 | 106 | 1.06 | 0.00000732 | 801 |
Loss of Function | 3.95 | 0 | 18.1 | 0.00 | 7.69e-7 | 218 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.000202 | 0.000199 |
East Asian | 0.000112 | 0.000109 |
Finnish | 0.0000488 | 0.0000464 |
European (Non-Finnish) | 0.0000182 | 0.0000176 |
Middle Eastern | 0.000112 | 0.000109 |
South Asian | 0.0000666 | 0.0000654 |
Other | 0.000169 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May play an important role in B-cell differentiation as well as neural development and spermatogenesis. Involved in the regulation of the CD19 gene, a B-lymphoid-specific target gene.;
- Disease
- DISEASE: Note=A chromosomal aberration involving PAX5 is a cause of acute lymphoblastic leukemia. Translocation t(9;18)(p13;q11.2) with ZNF521. Translocation t(9;3)(p13;p14.1) with FOXP1. Translocation t(9;12)(p13;p13) with ETV6. {ECO:0000269|PubMed:17344859}.; DISEASE: Leukemia, acute lymphoblastic, 3 (ALL3) [MIM:613065]: A subtype of acute leukemia, a cancer of the white blood cells. Acute lymphoblastic anemia is a malignant disease of bone marrow and the most common malignancy diagnosed in children. The malignant cells are lymphoid precursor cells (lymphoblasts) that are arrested in an early stage of development. The lymphoblasts replace the normal marrow elements, resulting in a marked decrease in the production of normal blood cells. Consequently, anemia, thrombocytopenia, and neutropenia occur to varying degrees. The lymphoblasts also proliferate in organs other than the marrow, particularly the liver, spleen, and lymphnodes. {ECO:0000269|PubMed:24013638}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Transcriptional misregulation in cancer - Homo sapiens (human);Prion disease pathway;ID signaling pathway;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates transcription of genes involved in BCR signaling;C-MYB transcription factor network;ID;Transcriptional regulation by RUNX1
(Consensus)
Recessive Scores
- pRec
- 0.0809
Intolerance Scores
- loftool
- 0.0277
- rvis_EVS
- 0
- rvis_percentile_EVS
- 53.73
Haploinsufficiency Scores
- pHI
- 0.437
- hipred
- Y
- hipred_score
- 0.875
- ghis
- 0.410
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pax5
- Phenotype
- neoplasm; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- pax5
- Affected structure
- hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- apoptotic
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;humoral immune response;multicellular organism development;spermatogenesis;aging;animal organ morphogenesis;lateral ventricle development;cerebral cortex development;adult behavior;skeletal muscle cell differentiation;positive regulation of transcription by RNA polymerase II;embryonic cranial skeleton morphogenesis;regulation of B cell receptor signaling pathway;negative regulation of histone H3-K9 methylation
- Cellular component
- fibrillar center;nucleoplasm;cytosol;intracellular membrane-bounded organelle
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding