MIB2

MIB E3 ubiquitin protein ligase 2, the group of Ankyrin repeat domain containing|Ring finger proteins|Zinc fingers ZZ-type

Basic information

Region (hg38): 1:1615454-1630605

Previous symbols: [ "ZZANK1" ]

Links

ENSG00000197530 ∙ NCBI:142678 ∙ OMIM:611141 ∙ HGNC:30577 ∙ Uniprot:Q96AX9 ∙ 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 MIB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIB2 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				9	6	15
missense			80	6	1	87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			12	3	1	16
Total	0	0	92	18	8

Variants in MIB2

This is a list of pathogenic ClinVar variants found in the MIB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1615464-C-CG			Benign (Dec 31, 2019)
1-1615470-C-A		not specified	Uncertain significance (May 12, 2024)
1-1615497-C-A		not specified	Uncertain significance (Apr 04, 2023)
1-1615511-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-1615512-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-1615514-A-G		not specified	Uncertain significance (Dec 20, 2022)
1-1615584-G-C		not specified	Uncertain significance (Jan 10, 2022)
1-1615602-T-C		not specified	Uncertain significance (Aug 01, 2022)
1-1615612-C-A		not specified	Likely benign (Dec 31, 2019)
1-1616568-C-G			Benign (Jun 29, 2018)
1-1616568-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-1616569-C-T		not specified	Uncertain significance (Jul 13, 2022)
1-1616577-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-1616601-G-C		not specified	Uncertain significance (Feb 12, 2024)
1-1616607-C-G		not specified	Uncertain significance (Mar 01, 2023)
1-1623402-C-T		not specified	Uncertain significance (Oct 18, 2021)
1-1623438-G-A		not specified	Uncertain significance (Mar 23, 2023)
1-1623445-C-T		not specified	Likely benign (Mar 07, 2024)
1-1623546-G-A		not specified	Uncertain significance (May 27, 2022)
1-1623567-C-G		not specified	Uncertain significance (Sep 12, 2023)
1-1623600-C-T		not specified	Uncertain significance (Dec 06, 2022)
1-1623616-A-C		not specified	Uncertain significance (May 25, 2022)
1-1623626-G-C		not specified	Likely benign (Apr 07, 2023)
1-1623633-C-T		not specified	Uncertain significance (Mar 04, 2024)
1-1623645-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIB2	protein_coding	protein_coding	ENST00000505820	20	15196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.80e-7	1.00	124036	7	574	124617	0.00233

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.623	644	690	0.933	0.0000494	6664
Missense in Polyphen		196	269.45	0.72741		2660
Synonymous	-3.36	395	319	1.24	0.0000251	2280
Loss of Function	3.59	19	45.0	0.422	0.00000237	476

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0315	0.0300
Ashkenazi Jewish	0.0000998	0.0000995
East Asian	0.000420	0.000390
Finnish	0.00173	0.00153
European (Non-Finnish)	0.000329	0.000283
Middle Eastern	0.000420	0.000390
South Asian	0.000408	0.000392
Other	0.000875	0.000825

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination of Delta receptors, which act as ligands of Notch proteins. Positively regulates the Delta-mediated Notch signaling by ubiquitinating the intracellular domain of Delta, leading to endocytosis of Delta receptors. {ECO:0000250|UniProtKB:Q8R516}.
• Pathway: NOTCH-Ncore;Disease;Signal Transduction;Immune System;Adaptive Immune System;Signaling by NOTCH1;Antigen processing: Ubiquitination & Proteasome degradation;Signaling by NOTCH2;NOTCH3 Activation and Transmission of Signal to the Nucleus;Class I MHC mediated antigen processing & presentation;Signaling by NOTCH3;Signaling by NOTCH;NOTCH2 Activation and Transmission of Signal to the Nucleus;Constitutive Signaling by NOTCH1 HD Domain Mutants;Signaling by NOTCH1 HD Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Diseases of signal transduction;Activated NOTCH1 Transmits Signal to the Nucleus (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.153
• rvis_EVS: -0.03
• rvis_percentile_EVS: 50.56

Haploinsufficiency Scores

• pHI: 0.176
• hipred: Y
• hipred_score: 0.639
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mib2
• Phenotype: homeostasis/metabolism phenotype; 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); 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein polyubiquitination;Notch signaling pathway;protein ubiquitination;positive regulation of I-kappaB kinase/NF-kappaB signaling
• Cellular component: ubiquitin ligase complex;cytoplasm;early endosome;cytosol
• Molecular function: actin binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding;ubiquitin protein ligase activity