TCERG1

protein-coding

transcription elongation regulator 1

Gene summary

This gene encodes a nuclear protein that regulates transcriptional elongation and pre-mRNA splicing. The encoded protein interacts with the hyperphosphorylated C-terminal domain of RNA polymerase II via multiple FF domains, and with the pre-mRNA splicing factor SF1 via a WW domain. Alternative splicing results in multiple transcripts variants encoding different isoforms. [provided by RefSeq, Jul 2008]

Previous symbols:

TAF2S

MANE transcript

NM_001382548.1

Inheritance

—

ClinVar variants

P:1U:114B:13

Top phenotype

Colorectal cancer

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr5:146,447,311-146,511,961

External References & Databases

Ensembl (ENSG00000113649)

Transcript & Mutation Effects

hg38 • Region Span ~64.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TCERG1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 14

Colorectal cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001382548.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	11 clinvar		16
missense			100 clinvar	1 clinvar	1 clinvar	102
nonsense						0
start loss						0
frameshift	1 clinvar		2 clinvar			3
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	1	0	114	12	1	128

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001382548.1	RefSeq	NP_001369477.1	23	MANE Select
ENST00000679501.2	Ensembl	ENSP00000505217.1	23	MANE Select
NM_001040006.2	RefSeq	NP_001035095.1	21	Standard
NM_001400077.1	RefSeq	NP_001387006.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)

Biological Process

negative regulation of transcription by RNA polymerase II
transcription by RNA polymerase II
positive regulation of nucleic acid-templated transcription

Molecular Function

RNA polymerase II repressing transcription factor binding
transcription coactivator activity
transcription corepressor activity
RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296702
Coding exons: 22
Length: 64651
Individuals with no LoFs: 125714
Homozygous LoFs: 2
Heterozygous LoFs: 32
Defined: 125748
p: 0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.34	366	595	0.615	0.0000334	7128
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00075	0.00069	rare
East Asian	0.00034	0.00022	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00017	0.00013	rare
South Asian	0.00017	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.238

Intolerance Scores

LoFtool: 0.571
RVIS EVS: -0.87
RVIS percentile EVS: 10.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.998

Gene Damage Prediction

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