MTA1
metastasis associated 1, the group of Myb/SANT domain containing|GATA zinc finger domain containing|NuRD complex subunits
Basic information
Region (hg38): 14:105419820-105470729
Links
Phenotypes
GenCC
Source:
No genCC data.
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 MTA1 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 | 28 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 28 | 1 | 2 |
Variants in MTA1
This is a list of pathogenic ClinVar variants found in the MTA1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-105445505-C-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 14-105449392-C-T | not specified | Uncertain significance (Apr 08, 2022) | ||
| 14-105450306-G-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| 14-105458272-G-A | not specified | Uncertain significance (Sep 26, 2022) | ||
| 14-105458330-C-G | not specified | Uncertain significance (Dec 13, 2023) | ||
| 14-105460414-G-A | not specified | Uncertain significance (Aug 10, 2021) | ||
| 14-105460892-A-G | not specified | Likely benign (Jul 15, 2021) | ||
| 14-105464044-T-G | not specified | Uncertain significance (Feb 14, 2024) | ||
| 14-105464060-G-A | not specified | Uncertain significance (Jul 23, 2024) | ||
| 14-105464078-G-A | not specified | Uncertain significance (Dec 02, 2024) | ||
| 14-105464093-A-C | not specified | Uncertain significance (Jan 03, 2022) | ||
| 14-105464680-C-T | not specified | Uncertain significance (Nov 07, 2024) | ||
| 14-105464683-G-A | not specified | Uncertain significance (Apr 06, 2022) | ||
| 14-105464689-C-G | not specified | Uncertain significance (Oct 22, 2021) | ||
| 14-105464714-A-C | not specified | Uncertain significance (Dec 06, 2021) | ||
| 14-105464714-A-G | not specified | Uncertain significance (Mar 08, 2024) | ||
| 14-105464753-C-T | not specified | Uncertain significance (Feb 02, 2022) | ||
| 14-105464765-C-T | not specified | Uncertain significance (Oct 26, 2021) | ||
| 14-105464788-C-T | not specified | Uncertain significance (Oct 30, 2024) | ||
| 14-105464792-A-G | not specified | Uncertain significance (Oct 21, 2024) | ||
| 14-105465141-C-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 14-105465148-T-C | not specified | Uncertain significance (Jun 05, 2024) | ||
| 14-105465168-G-C | not specified | Uncertain significance (Apr 04, 2023) | ||
| 14-105466437-C-T | not specified | Uncertain significance (Dec 27, 2022) | ||
| 14-105466443-C-G | not specified | Uncertain significance (Nov 21, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MTA1 | protein_coding | protein_coding | ENST00000331320 | 21 | 50908 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000108 | 125014 | 0 | 2 | 125016 | 0.00000800 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.50 | 271 | 489 | 0.554 | 0.0000349 | 4626 |
| Missense in Polyphen | 80 | 224.15 | 0.3569 | 2048 | ||
| Synonymous | -0.345 | 217 | 211 | 1.03 | 0.0000166 | 1402 |
| Loss of Function | 5.91 | 1 | 42.7 | 0.0234 | 0.00000213 | 486 |
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) | 0.00000888 | 0.00000888 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000371 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional coregulator which can act as both a transcriptional corepressor and coactivator. As a part of the histone-deacetylase multiprotein complex (NuRD), regulates transcription of its targets by modifying the acetylation status of the target chromatin and cofactor accessibility to the target DNA. In conjunction with other components of NuRD, acts as a transcriptional corepressor of BRCA1, ESR1, TFF1 and CDKN1A. Acts as a transcriptional coactivator of BCAS3, PAX5 and SUMO2, independent of the NuRD complex. Stimulates the expression of WNT1 by inhibiting the expression of its transcriptional corepressor SIX3. Regulates p53-dependent and -independent DNA repair processes following genotoxic stress. Regulates the stability and function of p53/TP53 by inhibiting its ubiquitination by COP1 and MDM2 thereby regulating the p53-dependent DNA repair. Plays an important role in tumorigenesis, tumor invasion, and metastasis. Involved in the epigenetic regulation of ESR1 expression in breast cancer in a TFAP2C, IFI16 and HDAC4/5/6-dependent manner. Plays a role in the regulation of the circadian clock and is essential for the generation and maintenance of circadian rhythms under constant light and for normal entrainment of behavior to light-dark (LD) cycles. Positively regulates the CLOCK-ARNTL/BMAL1 heterodimer mediated transcriptional activation of its own transcription and the transcription of CRY1. Regulates deacetylation of ARNTL/BMAL1 by regulating SIRT1 expression, resulting in derepressing CRY1- mediated transcription repression. Isoform Short binds to ESR1 and sequesters it in the cytoplasm and enhances its non-genomic responses. With TFCP2L1, promotes establishment and maintenance of pluripotency in embryonic stem cells (ESCs) and inhibits endoderm differentiation (By similarity). {ECO:0000250|UniProtKB:Q8K4B0, ECO:0000269|PubMed:16617102, ECO:0000269|PubMed:17671180, ECO:0000269|PubMed:17922032, ECO:0000269|PubMed:19837670, ECO:0000269|PubMed:21965678, ECO:0000269|PubMed:24413532}.;
- Pathway
- ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);SUMOylation of transcription factors;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;HDACs deacetylate histones;Metabolism of proteins;RNA Polymerase I Promoter Clearance;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;SUMOylation;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;Intracellular signaling by second messengers;Validated nuclear estrogen receptor alpha network;Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.226
Intolerance Scores
- loftool
- 0.0104
- rvis_EVS
- -1.06
- rvis_percentile_EVS
- 7.52
Haploinsufficiency Scores
- pHI
- 0.890
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.567
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.982
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mta1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; limbs/digits/tail phenotype; vision/eye phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;double-strand break repair;signal transduction;response to ionizing radiation;histone deacetylation;circadian regulation of gene expression;regulation of gene expression, epigenetic;entrainment of circadian clock by photoperiod;proteasome-mediated ubiquitin-dependent protein catabolic process;locomotor rhythm;positive regulation of protein autoubiquitination;positive regulation of nucleic acid-templated transcription
- Cellular component
- nucleus;nuclear envelope;nucleoplasm;cytoplasm;cytosol;microtubule;NuRD complex;intracellular membrane-bounded organelle
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II repressing transcription factor binding;chromatin binding;transcription coactivator activity;transcription corepressor activity;histone deacetylase activity;protein binding;zinc ion binding;histone deacetylase binding