MTDH
Basic information
Region (hg38): 8:97644184-97730260
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 MTDH 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 | 41 | 45 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 42 | 2 | 2 |
Variants in MTDH
This is a list of pathogenic ClinVar variants found in the MTDH region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
8-97644516-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
8-97644541-A-G | not specified | Uncertain significance (Jun 10, 2024) | ||
8-97644573-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
8-97644588-G-A | not specified | Uncertain significance (Jul 19, 2022) | ||
8-97644621-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
8-97644666-G-A | Benign (Dec 31, 2019) | |||
8-97644714-G-C | not specified | Uncertain significance (Nov 07, 2023) | ||
8-97644721-C-T | not specified | Uncertain significance (Mar 29, 2023) | ||
8-97644787-C-G | not specified | Uncertain significance (Nov 16, 2021) | ||
8-97644790-T-G | not specified | Uncertain significance (Aug 10, 2021) | ||
8-97644792-C-A | not specified | Uncertain significance (Oct 25, 2023) | ||
8-97644793-C-T | not specified | Uncertain significance (Nov 03, 2022) | ||
8-97644802-C-T | not specified | Uncertain significance (Oct 27, 2021) | ||
8-97644813-C-G | Benign (Mar 01, 2023) | |||
8-97661096-G-A | not specified | Uncertain significance (May 11, 2022) | ||
8-97661097-C-T | not specified | Uncertain significance (May 11, 2022) | ||
8-97661153-A-G | not specified | Uncertain significance (Jun 06, 2023) | ||
8-97661157-A-T | not specified | Uncertain significance (Apr 25, 2022) | ||
8-97661162-A-G | not specified | Uncertain significance (Jun 12, 2023) | ||
8-97686747-A-T | not specified | Uncertain significance (May 09, 2023) | ||
8-97687479-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
8-97687518-A-G | not specified | Uncertain significance (Jan 26, 2022) | ||
8-97687552-C-T | not specified | Uncertain significance (Apr 20, 2024) | ||
8-97687557-G-A | not specified | Uncertain significance (Apr 22, 2022) | ||
8-97687570-C-T | not specified | Uncertain significance (Jun 13, 2022) |
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