SNAI1
snail family transcriptional repressor 1, the group of SNAG transcriptional repressors|Zinc fingers C2H2-type
Basic information
Region (hg38): 20:49982980-49988886
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 SNAI1 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 | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 1 |
Variants in SNAI1
This is a list of pathogenic ClinVar variants found in the SNAI1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-49983133-C-G | not specified | Uncertain significance (Nov 08, 2024) | ||
| 20-49983938-C-T | Benign (Jul 13, 2018) | |||
| 20-49983994-G-A | not specified | Uncertain significance (Dec 27, 2023) | ||
| 20-49984045-C-T | not specified | Uncertain significance (May 26, 2024) | ||
| 20-49984073-C-T | not specified | Uncertain significance (Jan 24, 2025) | ||
| 20-49984082-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 20-49984087-A-G | not specified | Uncertain significance (Oct 12, 2024) | ||
| 20-49984106-A-G | not specified | Uncertain significance (Jun 05, 2023) | ||
| 20-49984115-C-T | not specified | Uncertain significance (Jun 16, 2024) | ||
| 20-49984198-G-A | not specified | Uncertain significance (Feb 26, 2025) | ||
| 20-49984261-C-G | not specified | Uncertain significance (Feb 27, 2023) | ||
| 20-49988025-A-T | not specified | Uncertain significance (Nov 07, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNAI1 | protein_coding | protein_coding | ENST00000244050 | 3 | 5888 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.218 | 0.775 | 125737 | 0 | 6 | 125743 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.31 | 112 | 159 | 0.706 | 0.00000915 | 1687 |
| Missense in Polyphen | 24 | 60.103 | 0.39932 | 591 | ||
| Synonymous | -0.657 | 78 | 71.0 | 1.10 | 0.00000423 | 559 |
| Loss of Function | 2.30 | 3 | 11.4 | 0.264 | 6.39e-7 | 106 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000271 | 0.0000264 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in induction of the epithelial to mesenchymal transition (EMT), formation and maintenance of embryonic mesoderm, growth arrest, survival and cell migration. Binds to 3 E-boxes of the E-cadherin/CDH1 gene promoter and to the promoters of CLDN7 and KRT8 and, in association with histone demethylase KDM1A which it recruits to the promoters, causes a decrease in dimethylated H3K4 levels and represses transcription. During EMT, involved with LOXL2 in negatively regulating pericentromeric heterochromatin transcription (By similarity). SNAI1 recruits LOXL2 to pericentromeric regions to oxidize histone H3 and repress transcription which leads to release of heterochromatin component CBX5/HP1A, enabling chromatin reorganization and acquisition of mesenchymal traits (By similarity). Associates with EGR1 and SP1 to mediate tetradecanoyl phorbol acetate (TPA)-induced up- regulation of CDKN2B, possibly by binding to the CDKN2B promoter region 5'-TCACA-3. In addition, may also activate the CDKN2B promoter by itself. {ECO:0000250|UniProtKB:Q02085, ECO:0000269|PubMed:10655587, ECO:0000269|PubMed:15647282, ECO:0000269|PubMed:16096638, ECO:0000269|PubMed:20121949, ECO:0000269|PubMed:20562920, ECO:0000269|PubMed:21952048}.;
- Pathway
- Adherens junction - Homo sapiens (human);Neural Crest Differentiation;Mesodermal Commitment Pathway;Kit receptor signaling pathway;TGF-B Signaling in Thyroid Cells for Epithelial-Mesenchymal Transition;EMT transition in Colorectal Cancer;Signal Transduction;downregulated of mta-3 in er-negative breast tumors;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Integrin-linked kinase signaling;Intracellular signaling by second messengers;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.331
Intolerance Scores
- loftool
- 0.232
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.146
- hipred
- Y
- hipred_score
- 0.798
- ghis
- 0.403
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.959
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snai1
- Phenotype
- skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); 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; embryo phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- snai1a
- Affected structure
- postcranial axial skeleton
- Phenotype tag
- abnormal
- Phenotype quality
- ossified
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;osteoblast differentiation;mesoderm formation;epithelial to mesenchymal transition;aortic valve morphogenesis;epithelial to mesenchymal transition involved in endocardial cushion formation;positive regulation of epithelial to mesenchymal transition;negative regulation of vitamin D biosynthetic process;cell migration;positive regulation of cell migration;hair follicle morphogenesis;negative regulation of DNA damage response, signal transduction by p53 class mediator;positive regulation of transcription, DNA-templated;roof of mouth development;cartilage morphogenesis;trophoblast giant cell differentiation;negative regulation of cell differentiation involved in embryonic placenta development;left/right pattern formation;Notch signaling involved in heart development;heterochromatin organization;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage;regulation of bicellular tight junction assembly
- Cellular component
- nucleus;nucleoplasm;pericentric heterochromatin;cytoplasm;cytosol
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;kinase binding;metal ion binding;E-box binding