MT3
metallothionein 3, the group of Metallothioneins
Basic information
Region (hg38): 16:56589074-56591088
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MT3 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 1 |
Variants in MT3
This is a list of pathogenic ClinVar variants found in the MT3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-56589613-G-A | not specified | Uncertain significance (Mar 21, 2022) | ||
| 16-56589930-A-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 16-56590846-G-T | not specified | Uncertain significance (May 26, 2023) | ||
| 16-56590861-C-T | not specified | Uncertain significance (Nov 15, 2021) | ||
| 16-56590917-G-A | not specified | Uncertain significance (Dec 19, 2023) | ||
| 16-56590942-G-A | Benign (Aug 01, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MT3 | protein_coding | protein_coding | ENST00000200691 | 3 | 2015 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0645 | 0.742 | 125706 | 0 | 6 | 125712 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.661 | 26 | 37.4 | 0.696 | 0.00000176 | 443 |
| Missense in Polyphen | 8 | 11.706 | 0.68344 | 148 | ||
| Synonymous | -0.587 | 17 | 14.2 | 1.20 | 7.87e-7 | 106 |
| Loss of Function | 0.869 | 2 | 3.84 | 0.521 | 1.61e-7 | 48 |
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 | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.00000901 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds heavy metals. Contains three zinc and three copper atoms per polypeptide chain and only a negligible amount of cadmium. Inhibits survival and neurite formation of cortical neurons in vitro.;
- Pathway
- Copper homeostasis;Zinc homeostasis;Response to metal ions;Cellular responses to external stimuli;Metallothioneins bind metals
(Consensus)
Recessive Scores
- pRec
- 0.260
Intolerance Scores
- loftool
- 0.625
- rvis_EVS
- 0.32
- rvis_percentile_EVS
- 72.94
Haploinsufficiency Scores
- pHI
- 0.140
- hipred
- N
- hipred_score
- 0.241
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mt3
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- obsolete protein import into nucleus, translocation;response to hypoxia;positive regulation of protein phosphorylation;energy reserve metabolic process;cholesterol catabolic process;zinc ion transport;cellular metal ion homeostasis;cellular zinc ion homeostasis;apoptotic process;brain development;cell population proliferation;response to metal ion;detoxification of copper ion;negative regulation of autophagy;positive regulation of gene expression;positive regulation of necrotic cell death;positive regulation of cell death;astrocyte development;histone modification;removal of superoxide radicals;negative regulation of cell growth;negative regulation of axon extension;positive regulation of vascular endothelial growth factor receptor signaling pathway;regulation of response to food;activation of protein kinase B activity;leptin-mediated signaling pathway;cellular response to oxidative stress;cellular response to drug;positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress;negative regulation of apoptotic process;positive regulation of catalytic activity;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;protein kinase B signaling;negative regulation of neuron apoptotic process;cellular lipid catabolic process;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;protein stabilization;negative regulation of oxidoreductase activity;zinc ion homeostasis;cadmium ion homeostasis;regulation of protein glycosylation;negative regulation of necrotic cell death;ERK1 and ERK2 cascade;positive regulation of ERK1 and ERK2 cascade;cellular response to cadmium ion;cellular response to copper ion;cellular response to zinc ion;cellular response to hypoxia;cellular response to nitric oxide;positive regulation of lysosomal membrane permeability;negative regulation of cysteine-type endopeptidase activity;negative regulation of hydrogen peroxide catabolic process;positive regulation of oxygen metabolic process;negative regulation of reactive oxygen species metabolic process
- Cellular component
- extracellular space;nucleus;cytoplasm;mitochondrial outer membrane;rough endoplasmic reticulum;cytosol;ribosome;microtubule;plasma membrane;synaptic vesicle;postsynaptic density;inclusion body;axon;dendritic spine;perinuclear region of cytoplasm;astrocyte end-foot
- Molecular function
- copper ion binding;protein binding;drug binding;zinc ion binding;antioxidant activity;protein kinase activator activity;cysteine-type endopeptidase inhibitor activity involved in apoptotic process;cadmium ion binding;metal ion binding