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

ENSG00000057657 ∙ NCBI:639 ∙ OMIM:603423 ∙ HGNC:9346 ∙ Uniprot:O75626 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRDM1 gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			32	5	3	40
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	7	4

Variants in PRDM1

This is a list of pathogenic ClinVar variants found in the PRDM1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-106086581-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-106088205-C-T		not specified	Uncertain significance (Mar 20, 2023)
6-106088211-A-G		not specified	Uncertain significance (Mar 20, 2023)
6-106088231-A-G		not specified	Uncertain significance (Oct 12, 2022)
6-106088233-G-C		not specified	Uncertain significance (Jun 06, 2023)
6-106088347-C-T		not specified	Likely benign (Apr 24, 2024)
6-106088378-G-A		not specified	not provided (Sep 19, 2013)
6-106088388-T-C		not specified	Uncertain significance (Apr 25, 2023)
6-106088397-A-T		PRDM1-related disorder	Likely benign (Jul 20, 2022)
6-106088408-C-G		not specified	Uncertain significance (Jun 03, 2022)
6-106088437-CA-C		not specified	Uncertain significance (Feb 19, 2019)
6-106095710-C-T			Benign (Dec 31, 2019)
6-106099313-G-A		not specified	Uncertain significance (May 02, 2024)
6-106099336-G-A		not specified	not provided (Sep 19, 2013)
6-106099388-C-T		not specified	Uncertain significance (May 28, 2024)
6-106099390-C-G		not specified	not provided (Sep 19, 2013)
6-106099492-C-T		not specified	Uncertain significance (Mar 25, 2024)
6-106099493-G-A		not specified	Uncertain significance (Jan 29, 2024)
6-106099497-C-G		not specified	Benign (Feb 18, 2020)
6-106099528-G-A		not specified	Uncertain significance (May 29, 2024)
6-106099540-A-G		not specified	Uncertain significance (Jan 30, 2024)
6-106104834-A-G		not specified	Uncertain significance (Jun 24, 2022)
6-106104900-A-G		not specified	Uncertain significance (Dec 01, 2022)
6-106104944-A-G		not specified	Uncertain significance (Dec 14, 2022)
6-106104971-A-G		not specified	Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

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: dbNSFP

• 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