TSC22D3
Basic information
Region (hg38): X:107713221-107777342
Previous symbols: [ "DSIPI" ]
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 TSC22D3 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 | 3 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 2 | 1 |
Variants in TSC22D3
This is a list of pathogenic ClinVar variants found in the TSC22D3 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-107714523-A-G | not specified | Uncertain significance (Dec 07, 2021) | ||
| X-107714525-C-T | Benign (Jul 05, 2018) | |||
| X-107714539-G-A | not specified | Uncertain significance (Aug 10, 2023) | ||
| X-107714541-G-A | not specified | Uncertain significance (Jul 28, 2021) | ||
| X-107714563-C-T | not specified | Uncertain significance (May 03, 2023) | ||
| X-107714629-T-A | not specified | Uncertain significance (Mar 24, 2023) | ||
| X-107714705-C-T | Likely benign (Apr 01, 2022) | |||
| X-107715906-T-C | not specified | Uncertain significance (Mar 14, 2023) | ||
| X-107775414-G-C | Likely benign (Apr 01, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TSC22D3 | protein_coding | protein_coding | ENST00000372383 | 3 | 64122 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.434 | 0.538 | 125708 | 0 | 2 | 125710 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 53 | 78.8 | 0.672 | 0.00000560 | 1311 |
| Missense in Polyphen | 10 | 25.233 | 0.39631 | 448 | ||
| Synonymous | -0.0498 | 36 | 35.6 | 1.01 | 0.00000263 | 406 |
| Loss of Function | 1.75 | 1 | 5.39 | 0.186 | 4.13e-7 | 79 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000365 | 0.0000365 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000721 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000721 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protects T-cells from IL2 deprivation-induced apoptosis through the inhibition of FOXO3A transcriptional activity that leads to the down-regulation of the pro-apoptotic factor BCL2L11. In macrophages, plays a role in the anti-inflammatory and immunosuppressive effects of glucocorticoids and IL10. In T-cells, inhibits anti-CD3-induced NFKB1 nuclear translocation. In vitro, suppresses AP1 and NFKB1 DNA-binding activities (By similarity). Isoform 1 inhibits myogenic differentiation and mediates anti- myogenic effects of glucocorticoids by binding and regulating MYOD1 and HDAC1 transcriptional activity resulting in reduced expression of MYOG (By similarity). {ECO:0000250, ECO:0000269|PubMed:15031210}.;
- Pathway
- Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Stimuli-sensing channels;Ion channel transport;Transport of small molecules
(Consensus)
Recessive Scores
- pRec
- 0.216
Intolerance Scores
- loftool
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.303
- hipred
- Y
- hipred_score
- 0.766
- ghis
- 0.576
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.956
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tsc22d3
- Phenotype
- liver/biliary system phenotype; reproductive system phenotype; hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;response to osmotic stress;ion transmembrane transport;negative regulation of activation-induced cell death of T cells
- Cellular component
- nucleus;cytosol
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity