MTSS1
Basic information
Region (hg38): 8:124550784-124728473
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (105 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTSS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014751.6. 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 | 5 | |||||
| missense | 101 | 103 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 101 | 7 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MTSS1 | protein_coding | protein_coding | ENST00000518547 | 14 | 177700 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000296 | 125744 | 0 | 2 | 125746 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.81 | 348 | 457 | 0.761 | 0.0000273 | 4890 |
| Missense in Polyphen | 141 | 219.9 | 0.6412 | 2257 | ||
| Synonymous | 0.989 | 159 | 176 | 0.905 | 0.0000108 | 1538 |
| Loss of Function | 5.14 | 3 | 36.5 | 0.0822 | 0.00000198 | 400 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000917 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be related to cancer progression or tumor metastasis in a variety of organ sites, most likely through an interaction with the actin cytoskeleton.;
- Pathway
- HH-Ncore;EGF-Ncore;Hedgehog signaling events mediated by Gli proteins
(Consensus)
Recessive Scores
- pRec
- 0.999
Intolerance Scores
- loftool
- 0.0290
- rvis_EVS
- -0.82
- rvis_percentile_EVS
- 11.94
Haploinsufficiency Scores
- pHI
- 0.371
- hipred
- Y
- hipred_score
- 0.725
- ghis
- 0.498
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.976
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mtss1
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; skeleton phenotype; renal/urinary system 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); hematopoietic system phenotype; neoplasm;
Gene ontology
- Biological process
- plasma membrane organization;cell adhesion;transmembrane receptor protein tyrosine kinase signaling pathway;microspike assembly;actin cytoskeleton organization;negative regulation of epithelial cell proliferation;renal tubule morphogenesis;cellular response to fluid shear stress;glomerulus morphogenesis;nephron tubule epithelial cell differentiation;epithelial cell proliferation involved in renal tubule morphogenesis
- Cellular component
- ruffle;cytoplasm;actin cytoskeleton;endocytic vesicle
- Molecular function
- actin monomer binding;signaling receptor binding;protein binding;identical protein binding