TCF19 transcription factor 19 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TCF19provided by HGNC
Official Full Name: transcription factor 19provided by HGNC
Primary source: HGNC:HGNC:11629
See related: Ensembl:ENSG00000137310 MIM:600912; AllianceGenome:HGNC:11629
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SC1; TCF-19
Summary: This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression: Ubiquitous expression in lymph node (RPKM 8.0), appendix (RPKM 5.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (31158589..31164215)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (31026273..31031895)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (31126366..31131992)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Genetic variants associated with expression of TCF19 contribute to the risk of head and neck cancer in Chinese population.
Title: Genetic variants associated with expression of TCF19 contribute to the risk of head and neck cancer in Chinese population.
Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes.
Title: Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes.
TCF19 and p53 regulate transcription of TIGAR and SCO2 in HCC for mitochondrial energy metabolism and stress adaptation.
Title: TCF19 and p53 regulate transcription of TIGAR and SCO2 in HCC for mitochondrial energy metabolism and stress adaptation.
TCF19 aggravates the malignant progression of colorectal cancer by negatively regulating WWC1.
Title: TCF19 aggravates the malignant progression of colorectal cancer by negatively regulating WWC1.
TCF19 Promotes Cell Proliferation through Binding to the Histone H3K4me3 Mark.
Title: TCF19 Promotes Cell Proliferation through Binding to the Histone H3K4me3 Mark.
AKT/FOXO1 signaling is essential for TCF19 influence on hepatocellular carcinoma progression
Title: TCF19 enhances cell proliferation in hepatocellular carcinoma by activating the ATK/FOXO1 signaling pathway.
Data suggest TCF19 interacts with histone 3 lysine 4 trimethylation through its plant homeodomain finger; TCF19 expression appears to regulate gluconeogenesis in hepatocytes; TCF19 interacts with CHD4 causing NuRD complex recruitment to gene promoters of enzymes involved in gluconeogenesis. (TCF19 = transcription factor 19; CHD4 = chromodomain helicase DNA binding protein 4; NuRD = nucleosome-remodeling-deacetylase)
Title: Transcription factor 19 interacts with histone 3 lysine 4 trimethylation and controls gluconeogenesis via the nucleosome-remodeling-deacetylase complex.
Genome association studies identified TCF19 as a new risk-associated loci for chronic hepatitis B on the HLA region of chromosome 6.
Title: A genome-wide association study identified new variants associated with the risk of chronic hepatitis B.
Data shows increased apoptosis and susceptibility to endoplasmic reticulum (ER) stress after Tcf19 knockdown.
Title: Tcf19 is a novel islet factor necessary for proliferation and survival in the INS-1 β-cell line.
Knockdown of Tcf19 reduces proliferation and increases apoptosis. Tcf19 is found in pancreatic islets in mouse and human.
Title: Tcf19 is a novel islet factor necessary for proliferation and survival in the INS-1 β-cell line.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identified new variants associated with the risk of chronic hepatitis B. EBI GWAS Catalog EBI GWAS CatalogPubMed
A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variation at 3q26.2, 6p21.33, 17p11.2 and 22q13.1 influences multiple myeloma risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis in Europe. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH46726 (e-PCR)
- UniSTS:57910

STS-U25826 (e-PCR)
- UniSTS:24119

G60011 (e-PCR)
- UniSTS:137279

RH36318 (e-PCR)
- UniSTS:75328

SHGC-12693 (e-PCR)
- UniSTS:38468

RH68003 (e-PCR)
- UniSTS:30891

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: transcription factor 19

Names: transcription factor SC1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001077511.2 → NP_001070979.1 transcription factor 19

See identical proteins and their annotated locations for NP_001070979.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein.

Source sequence(s)

AL662844, BC033086, BP365938, DA116232

Consensus CDS

CCDS43446.1

UniProtKB/Swiss-Prot

A6NCT8, B0UY11, Q0EFA8, Q13176, Q15967, Q5SQ89, Q5STD6, Q5STF5, Q9BUM2, Q9UBH7, Q9Y242

UniProtKB/TrEMBL

A0A0G2JH60, A0A1U9X8M7, D2IYK5

Related

ENSP00000365431.4, ENST00000376255.4

Conserved Domains (3) summary

cd00060
Location:5 → 122

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

cd15609
Location:291 → 339

PHD_TCF19; PHD finger found in Transcription factor 19 (TCF-19) and similar proteins

cl26464
Location:106 → 295

Atrophin-1; Atrophin-1 family
NM_001318908.2 → NP_001305837.1 transcription factor 19

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate segment in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein.

Source sequence(s)

AL662844, BC044632, BP365938, DA930848

Consensus CDS

CCDS43446.1

UniProtKB/Swiss-Prot

A6NCT8, B0UY11, Q0EFA8, Q13176, Q15967, Q5SQ89, Q5STD6, Q5STF5, Q9BUM2, Q9UBH7, Q9Y242

UniProtKB/TrEMBL

A0A0G2JH60, A0A1U9X8M7, D2IYK5

Related

ENSP00000516543.1, ENST00000706778.1

Conserved Domains (3) summary

cd00060
Location:5 → 122

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

cd15609
Location:291 → 339

PHD_TCF19; PHD finger found in Transcription factor 19 (TCF-19) and similar proteins

cl26464
Location:106 → 295

Atrophin-1; Atrophin-1 family
NM_007109.3 → NP_009040.2 transcription factor 19

See identical proteins and their annotated locations for NP_009040.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein.

Source sequence(s)

AL662844, BC033086, BP365938, DA115077, DA485961, DB260358

Consensus CDS

CCDS43446.1

UniProtKB/Swiss-Prot

A6NCT8, B0UY11, Q0EFA8, Q13176, Q15967, Q5SQ89, Q5STD6, Q5STF5, Q9BUM2, Q9UBH7, Q9Y242

UniProtKB/TrEMBL

A0A0G2JH60, A0A1U9X8M7, D2IYK5

Related

ENSP00000365433.3, ENST00000376257.8

Conserved Domains (3) summary

cd00060
Location:5 → 122

FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...

cd15609
Location:291 → 339

PHD_TCF19; PHD finger found in Transcription factor 19 (TCF-19) and similar proteins

cl26464
Location:106 → 295

Atrophin-1; Atrophin-1 family