MT4
Basic information
Region (hg38): 16:56565073-56568957
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 MT4 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 | 6 | 0 | 0 |
Variants in MT4
This is a list of pathogenic ClinVar variants found in the MT4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-56565156-T-A | not specified | Uncertain significance (Mar 24, 2023) | ||
16-56567790-C-G | not specified | Uncertain significance (Jan 05, 2022) | ||
16-56568858-C-T | not specified | Uncertain significance (Oct 25, 2024) | ||
16-56568862-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
16-56568880-C-T | not specified | Uncertain significance (Nov 26, 2024) | ||
16-56568895-G-A | not specified | Uncertain significance (Dec 01, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MT4 | protein_coding | protein_coding | ENST00000219162 | 3 | 3909 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000131 | 0.240 | 125123 | 0 | 152 | 125275 | 0.000607 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.360 | 40 | 34.1 | 1.17 | 0.00000169 | 405 |
Missense in Polyphen | 7 | 5.7659 | 1.214 | 59 | ||
Synonymous | -0.383 | 12 | 10.4 | 1.15 | 5.30e-7 | 92 |
Loss of Function | -0.746 | 5 | 3.49 | 1.43 | 1.46e-7 | 49 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00126 | 0.00124 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000471 | 0.0000462 |
European (Non-Finnish) | 0.000168 | 0.000159 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00376 | 0.00363 |
Other | 0.000171 | 0.000164 |
dbNSFP
Source:
- Function
- FUNCTION: Seems to bind zinc and copper. Could play a special role in regulating zinc metabolism during the differentiation of stratified epithelia.;
- Pathway
- Copper homeostasis;Zinc homeostasis;Response to metal ions;Cellular responses to external stimuli;Metallothioneins bind metals
(Consensus)
Recessive Scores
- pRec
- 0.253
Intolerance Scores
- loftool
- rvis_EVS
- 0.66
- rvis_percentile_EVS
- 84.27
Haploinsufficiency Scores
- pHI
- 0.271
- hipred
- N
- hipred_score
- 0.170
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0211
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mt4
- Phenotype
Gene ontology
- Biological process
- cellular zinc ion homeostasis;biological_process;detoxification of copper ion;cellular response to cadmium ion;cellular response to copper ion;cellular response to zinc ion
- Cellular component
- nucleus;cytoplasm
- Molecular function
- metal ion binding