MICB
Basic information
Region (hg38): 6:31494881-31511124
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (49 variants)
- not_provided (3 variants)
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. These statistics are base on transcript: NM_000005931.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 44 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 44 | 5 | 2 |
GnomAD
Source:
| 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:
- 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
- pHI
- 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
- Phenotype
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