TCEA1
transcription elongation factor A1, the group of General transcription factors
Basic information
Region (hg38): 8:53966552-54022448
Previous symbols: [ "TCEA", "GTF2S" ]
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 TCEA1 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 | 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 | 10 | 0 | 0 |
Variants in TCEA1
This is a list of pathogenic ClinVar variants found in the TCEA1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-53970412-C-G | not specified | Uncertain significance (Jan 18, 2022) | ||
| 8-53970453-C-T | not specified | Uncertain significance (Aug 02, 2023) | ||
| 8-53984428-T-C | not specified | Uncertain significance (Feb 27, 2023) | ||
| 8-53987011-T-C | not specified | Uncertain significance (May 26, 2023) | ||
| 8-53988219-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
| 8-53988235-G-T | not specified | Uncertain significance (May 26, 2023) | ||
| 8-53988245-T-C | not specified | Uncertain significance (Feb 01, 2023) | ||
| 8-53993693-T-G | not specified | Uncertain significance (Jun 22, 2024) | ||
| 8-53993705-T-C | not specified | Uncertain significance (Mar 25, 2022) | ||
| 8-53993733-G-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| 8-53999950-A-G | not specified | Uncertain significance (Oct 14, 2023) | ||
| 8-54000020-T-C | not specified | Uncertain significance (Dec 18, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TCEA1 | protein_coding | protein_coding | ENST00000521604 | 10 | 55978 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.895 | 0.105 | 124633 | 0 | 11 | 124644 | 0.0000441 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.38 | 104 | 152 | 0.685 | 0.00000768 | 1983 |
| Missense in Polyphen | 17 | 42.963 | 0.39569 | 619 | ||
| Synonymous | -0.0600 | 50 | 49.5 | 1.01 | 0.00000247 | 523 |
| Loss of Function | 3.26 | 2 | 16.1 | 0.124 | 8.07e-7 | 224 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000100 | 0.0000994 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000535 | 0.0000531 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000134 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.;
- Disease
- DISEASE: Note=A chromosomal aberration involving TCEA1 may be a cause of salivary gland pleiomorphic adenomas (PA) [181030]. Pleiomorphic adenomas are the most common benign epithelial tumors of the salivary gland. Translocation t(3;8)(p21;q12) with PLAG1. {ECO:0000269|PubMed:10029085}.;
- Pathway
- DNA Repair;Disease;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;HIV Transcription Elongation;HIV elongation arrest and recovery;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Transcription Elongation;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;Formation of TC-NER Pre-Incision Complex;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- loftool
- 0.279
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 73.97
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.641
- ghis
- 0.569
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tcea1
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; liver/biliary system phenotype; embryo phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype; 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);
Gene ontology
- Biological process
- transcription-coupled nucleotide-excision repair;regulation of transcription, DNA-templated;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;positive regulation of exoribonuclease activity
- Cellular component
- nucleus;nucleoplasm;transcription factor TFIID complex;nucleolus
- Molecular function
- DNA binding;protein binding;zinc ion binding