TCERG1

transcription elongation regulator 1

Basic information

Region (hg38): 5:146447311-146511961

Previous symbols: [ "TAF2S" ]

Links

ENSG00000113649 ∙ NCBI:10915 ∙ OMIM:605409 ∙ HGNC:15630 ∙ Uniprot:O14776 ∙ 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 TCERG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCERG1 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				9		9
missense			36		1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	9	1

Variants in TCERG1

This is a list of pathogenic ClinVar variants found in the TCERG1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-146447359-C-G		not specified	Uncertain significance (Jun 11, 2021)
5-146447371-G-T		not specified	Uncertain significance (Apr 25, 2023)
5-146455091-C-T		not specified	Uncertain significance (Apr 17, 2024)
5-146455092-G-A			Likely benign (Dec 01, 2022)
5-146455186-CG-C		Colorectal cancer	Pathogenic (-)
5-146458888-A-G		not specified	Uncertain significance (Apr 23, 2024)
5-146458902-C-T		not specified	Uncertain significance (Dec 02, 2022)
5-146458924-C-T		not specified	Uncertain significance (Oct 26, 2021)
5-146459029-C-T		not specified	Uncertain significance (Feb 05, 2024)
5-146459037-C-G		not specified	Uncertain significance (Mar 16, 2024)
5-146459059-C-T		not specified	Uncertain significance (Apr 22, 2022)
5-146459066-T-C			Likely benign (Feb 01, 2023)
5-146459066-T-G			Likely benign (Feb 01, 2023)
5-146459075-G-A			Likely benign (Feb 01, 2023)
5-146459081-G-A			Likely benign (Feb 01, 2023)
5-146459084-C-A			Likely benign (Feb 01, 2023)
5-146459087-G-A			Likely benign (Feb 01, 2023)
5-146459179-C-T		not specified	Uncertain significance (Dec 15, 2023)
5-146459203-C-T		not specified	Uncertain significance (Oct 25, 2022)
5-146459266-C-A		not specified	Uncertain significance (Jul 26, 2022)
5-146459281-C-T			Benign (Apr 04, 2018)
5-146463569-A-G		not specified	Uncertain significance (Mar 22, 2023)
5-146463644-T-C		not specified	Uncertain significance (Nov 09, 2022)
5-146463647-A-C		not specified	Uncertain significance (Oct 26, 2022)
5-146463648-A-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCERG1	protein_coding	protein_coding	ENST00000296702	22	64651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000436	125714	2	32	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.34	366	595	0.615	0.0000334	7128
Missense in Polyphen		5	18.595	0.26889		184
Synonymous	-1.04	222	203	1.09	0.0000114	2106
Loss of Function	6.47	8	63.7	0.126	0.00000391	712

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000123
Ashkenazi Jewish	0.000752	0.000695
East Asian	0.000340	0.000217
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000166	0.000132
Middle Eastern	0.000340	0.000217
South Asian	0.000169	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds RNA polymerase II and inhibits the elongation of transcripts from target promoters. Regulates transcription elongation in a TATA box-dependent manner. Necessary for TAT-dependent activation of the human immunodeficiency virus type 1 (HIV-1) promoter. {ECO:0000269|PubMed:11604498, ECO:0000269|PubMed:9315662}.
• Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.238

Intolerance Scores

• loftool: 0.571
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.8

Haploinsufficiency Scores

• pHI: 0.947
• hipred: Y
• hipred_score: 0.749
• ghis: 0.679

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tcerg1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II repressing transcription factor binding;transcription coactivator activity;transcription corepressor activity;RNA binding;protein binding;identical protein binding;proline-rich region binding