MTDH
metadherin
Basic information
Region (hg38): 8:97644184-97730260
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (79 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTDH gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178812.4. 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 | 0 | |||||
| missense | 77 | 81 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 78 | 2 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MTDH | protein_coding | protein_coding | ENST00000336273 | 12 | 84592 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.329 | 0.671 | 125731 | 0 | 16 | 125747 | 0.0000636 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 250 | 299 | 0.835 | 0.0000151 | 3734 |
| Missense in Polyphen | 89 | 120.22 | 0.74033 | 1531 | ||
| Synonymous | 0.884 | 103 | 115 | 0.895 | 0.00000591 | 1136 |
| Loss of Function | 3.94 | 7 | 30.5 | 0.229 | 0.00000146 | 371 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000621 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000167 | 0.000163 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000445 | 0.0000439 |
| Middle Eastern | 0.000167 | 0.000163 |
| South Asian | 0.000141 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Downregulates SLC1A2/EAAT2 promoter activity when expressed ectopically. Activates the nuclear factor kappa-B (NF- kappa-B) transcription factor. Promotes anchorage-independent growth of immortalized melanocytes and astrocytes which is a key component in tumor cell expansion. Promotes lung metastasis and also has an effect on bone and brain metastasis, possibly by enhancing the seeding of tumor cells to the target organ endothelium. Induces chemoresistance. {ECO:0000269|PubMed:15927426, ECO:0000269|PubMed:16452207, ECO:0000269|PubMed:18316612, ECO:0000269|PubMed:19111877}.;
- Pathway
- Gastric Cancer Network 2;Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.143
Intolerance Scores
- loftool
- 0.541
- rvis_EVS
- -0.42
- rvis_percentile_EVS
- 25.56
Haploinsufficiency Scores
- pHI
- 0.422
- hipred
- Y
- hipred_score
- 0.546
- ghis
- 0.604
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mtdh
- Phenotype
- immune system phenotype; liver/biliary system phenotype; neoplasm; 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); normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); reproductive system phenotype; hematopoietic system phenotype; 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); cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;positive regulation of autophagy;lipopolysaccharide-mediated signaling pathway;negative regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of angiogenesis;positive regulation of NF-kappaB transcription factor activity;positive regulation of protein kinase B signaling;bicellular tight junction assembly;positive regulation of nucleic acid-templated transcription
- Cellular component
- fibrillar center;nucleus;cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;bicellular tight junction;integral component of membrane;apical plasma membrane;nuclear body;nuclear membrane;intercellular canaliculus;perinuclear region of cytoplasm
- Molecular function
- RNA polymerase II transcription factor binding;transcription coactivator activity;RNA binding;double-stranded RNA binding;protein binding;NF-kappaB binding