MICB

MHC class I polypeptide-related sequence B, the group of C1-set domain containing

Basic information

Region (hg38): 6:31494881-31511124

Links

ENSG00000204516 ∙ NCBI:4277 ∙ OMIM:602436 ∙ HGNC:7091 ∙ Uniprot:Q29980 ∙ 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 MICB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MICB 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	2
missense			20	4		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	4	2

Variants in MICB

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

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

Position	Type	Phenotype	Significance	ClinVar
6-31498204-G-A		not specified	Uncertain significance (Oct 06, 2021)
6-31498258-C-A		not specified	Uncertain significance (Dec 20, 2023)
6-31498259-C-T			Benign (Feb 09, 2018)
6-31505653-C-T		not specified	Uncertain significance (Oct 18, 2021)
6-31505685-G-A		not specified	Uncertain significance (Nov 02, 2023)
6-31505719-G-A		not specified	Likely benign (Oct 13, 2023)
6-31505737-G-A		not specified	Uncertain significance (Dec 15, 2022)
6-31505796-A-G		not specified	Uncertain significance (Sep 30, 2021)
6-31505805-G-A		not specified	Uncertain significance (Oct 26, 2021)
6-31505823-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-31506143-G-A		not specified	Uncertain significance (Oct 06, 2023)
6-31506208-C-T		not specified	Likely benign (Feb 06, 2023)
6-31506209-G-A		not specified	Uncertain significance (May 15, 2024)
6-31506266-C-T		not specified	Uncertain significance (May 15, 2024)
6-31506310-G-A		not specified	Likely benign (Feb 11, 2022)
6-31506328-G-A		not specified	Uncertain significance (Aug 04, 2024)
6-31506353-A-G		not specified	Uncertain significance (May 22, 2023)
6-31506359-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-31506412-G-T		not specified	Uncertain significance (Jan 08, 2024)
6-31507075-G-A		not specified	Uncertain significance (Jul 06, 2022)
6-31507126-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-31507141-T-A		not specified	Uncertain significance (Aug 26, 2024)
6-31507199-A-G		not specified	Uncertain significance (Jan 10, 2022)
6-31507221-G-C		not specified	Uncertain significance (Mar 01, 2024)
6-31507223-T-A		not specified	Uncertain significance (Sep 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MICB	protein_coding	protein_coding	ENST00000252229	6	16244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000406	0.852	124743	0	7	124750	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.554	194	217	0.894	0.0000116	2469
Missense in Polyphen		106	112.43	0.94282		1448
Synonymous	0.724	79	87.6	0.902	0.00000476	772
Loss of Function	1.36	9	14.6	0.615	6.25e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000540	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to have no role in antigen presentation. Acts as a stress-induced self-antigen that is recognized by gamma delta T cells. Ligand for the KLRK1/NKG2D receptor. Binding to KLRK1 leads to cell lysis. {ECO:0000269|PubMed:11491531, ECO:0000269|PubMed:11777960, ECO:0000269|PubMed:9497295}.
• Disease: DISEASE: Rheumatoid arthritis (RA) [MIM:180300]: An inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures. {ECO:0000269|PubMed:17003176}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. The MICB*004 allele is associated with rheumatoid arthritis.; DISEASE: Note=Genetic variation in MICB is associated with cytomegalovirus and herpes simplex virus I seropositivity and this may be associated with schizophrenia risk.
• Pathway: Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.840
• rvis_EVS: 1.82
• rvis_percentile_EVS: 96.99

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.178

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mill2

Gene ontology

• Biological process: T cell mediated cytotoxicity;immune response-activating cell surface receptor signaling pathway;immune response;response to oxidative stress;response to heat;viral process;cytolysis;natural killer cell activation;response to retinoic acid;natural killer cell mediated cytotoxicity;susceptibility to natural killer cell mediated cytotoxicity;gamma-delta T cell activation;negative regulation of defense response to virus by host;regulation of immune response
• Cellular component: extracellular space;plasma membrane;external side of plasma membrane;cell surface;integral component of membrane
• Molecular function: natural killer cell lectin-like receptor binding