COMMD3-BMI1

protein-coding

COMMD3-BMI1 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring COMM domain-containing protein 3 and polycomb complex protein BMI-1 genes on chromosome 10. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Feb 2011]

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:3B:1

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr10:22,316,388-22,329,542

External References & Databases

Ensembl (ENSG00000269897)

NCBI Gene (100532731)

HGNC:48326

GenCC

ClinVar (COMMD3-BMI1)

Transcript & Mutation Effects

hg38 • Region Span ~13.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COMMD3-BMI1 variants in ClinVar

3 Conditions Cataloged

Inborn genetic diseasesTotal: 3

not providedTotal: 2

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)				1 clinvar		1
Total	0	0	3	1	0	4

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001204062.2	RefSeq	NP_001190991.1	14	Standard
ENST00000417470.1	Ensembl	ENSP00000398759.2	2	Standard
ENST00000475460.6	Ensembl	ENSP00000473382.1	5	Standard
ENST00000489125.2	Ensembl	ENSP00000473495.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

negative regulation of transcription by RNA polymerase II
chromatin silencing
histone H2A-K119 monoubiquitination

Molecular Function

promoter-specific chromatin binding

Cellular Component

cytosol
nuclear body
PRC1 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000602390
Coding exons: 14
Length: 13155
Individuals with no LoFs: 125591
Homozygous LoFs: 0
Heterozygous LoFs: 157
Defined: 125748
p: 0.000624

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.90	163	247	0.659	0.0000116	3088
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0058	0.0057	notable
Latino/Admixed American	0.00035	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00038	0.00038	rare
South Asian	0.00014	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Essentials

Essential (CRISPR): N

Gene Damage Prediction

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