MT1X
Basic information
Region (hg38): 16:56682469-56684196
Previous symbols: [ "MT1" ]
Links
Phenotypes
GenCC
Source:
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 MT1X 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 1 | 0 |
Variants in MT1X
This is a list of pathogenic ClinVar variants found in the MT1X region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-56682560-G-C | not specified | Uncertain significance (Jun 06, 2022) | ||
| 16-56683200-A-G | not specified | Uncertain significance (May 17, 2023) | ||
| 16-56683239-A-G | MT1X-related disorder | Likely benign (Mar 29, 2019) | ||
| 16-56683993-T-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 16-56684030-A-T | not specified | Uncertain significance (Mar 21, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MT1X | protein_coding | protein_coding | ENST00000394485 | 3 | 1773 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000934 | 0.369 | 125615 | 0 | 124 | 125739 | 0.000493 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.238 | 29 | 32.8 | 0.883 | 0.00000154 | 397 |
| Missense in Polyphen | 4 | 4.6175 | 0.86627 | 44 | ||
| Synonymous | -0.388 | 15 | 13.2 | 1.14 | 7.04e-7 | 101 |
| Loss of Function | -0.413 | 4 | 3.20 | 1.25 | 1.35e-7 | 44 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000495 | 0.000495 |
| Ashkenazi Jewish | 0.00179 | 0.00179 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000668 | 0.000668 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000327 | 0.000327 |
| Other | 0.000652 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids. May be involved in FAM168A anti-apoptotic signaling (PubMed:23251525). {ECO:0000269|PubMed:23251525}.;
- Pathway
- Mineral absorption - Homo sapiens (human);Copper homeostasis;Zinc homeostasis;Oxidative Stress;Response to metal ions;Cellular responses to external stimuli;Metallothioneins bind metals
(Consensus)
Intolerance Scores
- loftool
- 0.721
- rvis_EVS
- 0.24
- rvis_percentile_EVS
- 68.72
Haploinsufficiency Scores
- pHI
- 0.117
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.393
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.575
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mt1
- Phenotype
- vision/eye phenotype; digestive/alimentary 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); skeleton phenotype; renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; reproductive system phenotype; normal phenotype; 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; cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- cellular zinc ion homeostasis;response to metal ion;detoxification of copper ion;cellular response to erythropoietin;negative regulation of growth;cellular response to cadmium ion;cellular response to copper ion;cellular response to zinc ion
- Cellular component
- nucleus;cytoplasm;perinuclear region of cytoplasm
- Molecular function
- protein binding;zinc ion binding;metal ion binding