PRDM1
PR/SET domain 1, the group of PR/SET domain family|Zinc fingers C2H2-type
Basic information
Region (hg38): 6:105993463-106109939
Previous symbols: [ "BLIMP1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (90 variants)
- not_provided (7 variants)
- PRDM1-related_disorder (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001198.4. 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 | 5 | |||||
| missense | 84 | 91 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 85 | 9 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRDM1 | protein_coding | protein_coding | ENST00000369096 | 7 | 23620 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.957 | 0.0435 | 125720 | 0 | 27 | 125747 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.77 | 380 | 490 | 0.775 | 0.0000300 | 5444 |
| Missense in Polyphen | 87 | 161.71 | 0.53801 | 1848 | ||
| Synonymous | 1.54 | 181 | 209 | 0.865 | 0.0000148 | 1631 |
| Loss of Function | 4.15 | 4 | 27.5 | 0.146 | 0.00000135 | 356 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00126 | 0.00125 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000476 | 0.0000462 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that mediates a transcriptional program in various innate and adaptive immune tissue-resident lymphocyte T cell types such as tissue-resident memory T (Trm), natural killer (trNK) and natural killer T (NKT) cells and negatively regulates gene expression of proteins that promote the egress of tissue-resident T-cell populations from non-lymphoid organs. Plays a role in the development, retention and long-term establishment of adaptive and innate tissue-resident lymphocyte T cell types in non-lymphoid organs, such as the skin and gut, but also in other nonbarrier tissues like liver and kidney, and therefore may provide immediate immunological protection against reactivating infections or viral reinfection (By similarity). Binds specifically to the PRDI element in the promoter of the beta-interferon gene (PubMed:1851123). Drives the maturation of B- lymphocytes into Ig secreting cells (PubMed:12626569). Associates with the transcriptional repressor ZNF683 to chromatin at gene promoter regions (By similarity). {ECO:0000250|UniProtKB:Q60636, ECO:0000269|PubMed:12626569, ECO:0000269|PubMed:1851123}.;
- Pathway
- Nucleotide-binding Oligomerization Domain (NOD) pathway;Vitamin D Receptor Pathway;IL-6 signaling pathway;Regulation of TP53 Expression and Degradation;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of TP53 Expression;Regulation of TP53 Expression and Degradation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Direct p53 effectors
(Consensus)
Recessive Scores
- pRec
- 0.348
Intolerance Scores
- loftool
- 0.0327
- rvis_EVS
- 0.82
- rvis_percentile_EVS
- 88.07
Haploinsufficiency Scores
- pHI
- 0.757
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.423
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
- Prdm1
- Phenotype
- limbs/digits/tail phenotype; renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; embryo phenotype; neoplasm; normal 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); reproductive system phenotype; growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- prdm1a
- Affected structure
- secondary motor neuron
- Phenotype tag
- abnormal
- Phenotype quality
- defasciculated
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;morphogenesis of a branching structure;maternal placenta development;adaptive immune response;heart valve development;ventricular septum development;germ cell development;post-embryonic development;positive regulation of gene expression;methylation;regulation of natural killer cell differentiation;regulation of extrathymic T cell differentiation;aorta development;regulation of cell population proliferation;eye photoreceptor cell development;innate immune response;cell fate commitment;artery morphogenesis;regulation of NK T cell differentiation;intestinal epithelial cell development;trophoblast giant cell differentiation;coronary vasculature development;sebum secreting cell proliferation
- Cellular component
- nucleus;nucleoplasm;cytoplasm
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;methyltransferase activity;chromatin DNA binding;histone deacetylase binding;sequence-specific DNA binding;metal ion binding;promoter-specific chromatin binding