MCTS1
MCTS1 re-initiation and release factor
Basic information
Region (hg38): X:120594010-120621159
Links
Phenotypes
GenCC
Source:
- immunodeficiency 118 (Moderate), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Immunodeficiency 118, mycobacteriosis | XL | Allergy/Immunology/Infectious | Individuals have been described as being at increased risk of disseminated mycobacterial infections including after BCG vaccination, and awareness may allow preventative measures and early and aggressive treatment of infections | Allergy/Immunology/Infectious | 37875108 |
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 MCTS1 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 | 1 | |||||
| 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 | 1 |
Variants in MCTS1
This is a list of pathogenic ClinVar variants found in the MCTS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-120605465-G-T | Inborn genetic diseases | Uncertain significance (Sep 28, 2022) | ||
| X-120605538-A-T | Inborn genetic diseases | Uncertain significance (Nov 27, 2024) | ||
| X-120605559-GGTAA-G | Immunodeficiency 118 | Pathogenic (Jan 24, 2024) | ||
| X-120606121-C-CT | Immunodeficiency 118 | Pathogenic (Jan 24, 2024) | ||
| X-120606129-G-A | Benign (Dec 31, 2019) | |||
| X-120606139-A-AG | Immunodeficiency 118 | Pathogenic (Jan 24, 2024) | ||
| X-120608238-G-T | Likely benign (Dec 01, 2022) | |||
| X-120612190-G-A | Inborn genetic diseases | Uncertain significance (Mar 04, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MCTS1 | protein_coding | protein_coding | ENST00000371315 | 6 | 27065 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.875 | 0.124 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.05 | 15 | 59.4 | 0.253 | 0.00000381 | 1202 |
| Missense in Polyphen | 0 | 14.373 | 0 | 309 | ||
| Synonymous | 0.860 | 14 | 18.7 | 0.747 | 0.00000119 | 318 |
| Loss of Function | 2.41 | 0 | 6.78 | 0.00 | 4.99e-7 | 135 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Anti-oncogene that plays a role in cell cycle regulation; decreases cell doubling time and anchorage-dependent growth; shortens the duration of G1 transit time and G1/S transition. When constitutively expressed, increases CDK4 and CDK6 kinases activity and CCND1/cyclin D1 protein level, as well as G1 cyclin/CDK complex formation. Involved in translation initiation; promotes recruitment of aminoacetyled initiator tRNA to P site of 40S ribosomes. Can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes into subunits. Plays a role as translation enhancer; recruits the density-regulated protein/DENR and binds to the cap complex of the 5'-terminus of mRNAs, subsequently altering the mRNA translation profile; up- regulates protein levels of BCL2L2, TFDP1, MRE11, CCND1 and E2F1, while mRNA levels remains constant. Hyperactivates DNA damage signaling pathway; increased gamma-irradiation-induced phosphorylation of histone H2AX, and induces damage foci formation. Increases the overall number of chromosomal abnormalities such as larger chromosomes formation and multiples chromosomal fusions when overexpressed in gamma-irradiated cells. May play a role in promoting lymphoid tumor development: lymphoid cell lines overexpressing MCTS1 exhibit increased growth rates and display increased protection against apoptosis. May contribute to the pathogenesis and progression of breast cancer via promotion of angiogenesis through the decline of inhibitory THBS1/thrombospondin-1, and inhibition of apoptosis. Involved in the process of proteasome degradation to down-regulate Tumor suppressor p53/TP53 in breast cancer cell; Positively regulates phosphorylation of MAPK1 and MAPK3. Involved in translation initiation; promotes aminoacetyled initiator tRNA to P site of 40S ribosomes. Can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes into subunits. {ECO:0000269|PubMed:10440924, ECO:0000269|PubMed:11709712, ECO:0000269|PubMed:12637315, ECO:0000269|PubMed:15897892, ECO:0000269|PubMed:16322206, ECO:0000269|PubMed:16982740, ECO:0000269|PubMed:17016429, ECO:0000269|PubMed:17416211, ECO:0000269|PubMed:20713520, ECO:0000269|PubMed:9766643}.;
Recessive Scores
- pRec
- 0.198
Intolerance Scores
- loftool
- rvis_EVS
- 0.32
- rvis_percentile_EVS
- 72.94
Haploinsufficiency Scores
- pHI
- 0.589
- hipred
- Y
- hipred_score
- 0.543
- ghis
- 0.410
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- 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
- Mcts1
- Phenotype
Gene ontology
- Biological process
- formation of translation preinitiation complex;translation reinitiation;cellular response to DNA damage stimulus;cell cycle;positive regulation of cell population proliferation;ribosome disassembly;regulation of growth;IRES-dependent viral translational initiation
- Cellular component
- cytosol;plasma membrane;cytosolic small ribosomal subunit
- Molecular function
- translation initiation factor activity;protein binding