COMMD3-BMI1

COMMD3-BMI1 readthrough

Basic information

Region (hg38): 10:22316387-22329542

Links

ENSG00000269897 ∙ NCBI:100532731 ∙ ∙ HGNC:48326 ∙ ∙ ∙ 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 COMMD3-BMI1 gene.

• Inborn genetic diseases (3 variants)
• not provided (2 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMMD3-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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding			1		1	2
Total	0	0	4	1	1

Variants in COMMD3-BMI1

This is a list of pathogenic ClinVar variants found in the COMMD3-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
10-22316423-G-T		not specified	Uncertain significance (Apr 19, 2023)
10-22318820-T-G		not specified	Uncertain significance (Feb 22, 2023)
10-22318964-T-C		not specified	Uncertain significance (May 25, 2022)
10-22318977-T-C		not specified	Likely benign (Jun 16, 2024)
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
COMMD3-BMI1	protein_coding	protein_coding	ENST00000602390	14	13155

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00150	0.998	125591	0	157	125748	0.000624

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	163	247	0.659	0.0000116	3088
Missense in Polyphen		15	54.058	0.27748		731
Synonymous	-1.06	98	85.6	1.15	0.00000402	868
Loss of Function	3.18	10	28.3	0.354	0.00000163	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00618	0.00603
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000380	0.000378
Middle Eastern	0.000220	0.000217
South Asian	0.000135	0.000131
Other	0.000326	0.000326

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);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)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.403

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin silencing;histone H2A-K119 monoubiquitination
• Cellular component: cytosol;nuclear body;PRC1 complex
• Molecular function: promoter-specific chromatin binding