TCEA1

transcription elongation factor A1, the group of General transcription factors

Basic information

Region (hg38): 8:53966551-54022456

Previous symbols: [ "TCEA", "GTF2S" ]

Links

ENSG00000187735 ∙ NCBI:6917 ∙ OMIM:601425 ∙ HGNC:11612 ∙ Uniprot:P23193 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TCEA1 gene.

• Inborn genetic diseases (6 variants)

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			6			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	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)
8-53993705-T-C		not specified	Uncertain significance (Mar 25, 2022)
8-53999950-A-G		not specified	Uncertain significance (Oct 14, 2023)
8-54000020-T-C		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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