BMI1

BMI1 proto-oncogene, polycomb ring finger, the group of Ring finger proteins|Polycomb group ring fingers

Basic information

Region (hg38): 10:22321098-22331484

Previous symbols: [ "PCGF4" ]

Links

ENSG00000168283 ∙ NCBI:648 ∙ OMIM:164831 ∙ HGNC:1066 ∙ Uniprot:P35226 ∙ 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 BMI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMI1 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						0
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1		1	2
Total	0	0	2	0	1

Variants in BMI1

This is a list of pathogenic ClinVar variants found in the BMI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-22326438-T-C		not specified	Uncertain significance (Dec 15, 2023)
10-22326561-T-G		See cases	Uncertain significance (Nov 26, 2018)
10-22326571-G-A			Benign (Jul 31, 2018)
10-22328706-C-T			Likely benign (Jun 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMI1	protein_coding	protein_coding	ENST00000376663	9	10274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.943	0.0571	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	84	174	0.482	0.00000826	2161
Missense in Polyphen		9	38.718	0.23245		500
Synonymous	-0.423	62	57.9	1.07	0.00000273	598
Loss of Function	3.48	2	17.9	0.112	0.00000105	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000236	0.000236
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000439
Middle Eastern	0.000109	0.000109
South Asian	0.0000370	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility (PubMed:15386022, PubMed:16359901, PubMed:26151332, PubMed:16714294, PubMed:21772249, PubMed:25355358, PubMed:27827373). The complex composed of RNF2, UB2D3 and BMI1 binds nucleosomes, and has activity only with nucleosomal histone H2A (PubMed:21772249, PubMed:25355358). In the PRC1-like complex, regulates the E3 ubiquitin-protein ligase activity of RNF2/RING2 (PubMed:15386022, PubMed:26151332, PubMed:21772249). {ECO:0000269|PubMed:15386022, ECO:0000269|PubMed:16359901, ECO:0000269|PubMed:16714294, ECO:0000269|PubMed:16882984, ECO:0000269|PubMed:21772249, ECO:0000269|PubMed:25355358, ECO:0000269|PubMed:26151332, ECO:0000269|PubMed:27827373}.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Senescence and Autophagy in Cancer;Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;the prc2 complex sets long-term gene silencing through modification of histone tails;Transcriptional Regulation by E2F6;Generic Transcription Pathway;Oxidative Stress Induced Senescence;SUMOylation of DNA damage response and repair proteins;Cellular Senescence;SUMOylation of chromatin organization proteins;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers;Transcriptional regulation by RUNX1;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.388

Intolerance Scores

• loftool: 0.348
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.242
• hipred: Y
• hipred_score: 0.743
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Mouse Genome Informatics

• Gene name: Bmi1
• Phenotype: craniofacial phenotype; cellular phenotype; endocrine/exocrine gland 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; 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); growth/size/body region phenotype; vision/eye 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin silencing;segment specification;regulation of gene expression;hemopoiesis;histone H2A-K119 monoubiquitination;negative regulation of gene expression, epigenetic;positive regulation of fibroblast proliferation;positive regulation of ubiquitin-protein transferase activity;negative regulation of G0 to G1 transition
• Cellular component: ubiquitin ligase complex;nucleus;nucleoplasm;cytosol;nuclear body;PcG protein complex;PRC1 complex
• Molecular function: protein binding;zinc ion binding;RING-like zinc finger domain binding;promoter-specific chromatin binding