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TCF19 transcription factor 19 [ Homo sapiens (human) ]

Gene ID: 6941, updated on 29-Mar-2023

Summary

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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

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See TCF19 in Genome Data Viewer
Location:
6p21.33
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31158589..31164215)
RS_2023_03 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_000006.12Genomic Context describing neighboring genes Neighboring gene coiled-coil alpha-helical rod protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31124820-31125320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31125321-31125821 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr6:31128969-31129952 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr6:31129953-31130936 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr6:31132319-31132900 Neighboring gene POU class 5 homeobox 1 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:31135533-31136390

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Genetic variants associated with expression of TCF19 contribute to the risk of head and neck cancer in Chinese population. Ji P, et al. J Med Genet, 2022 Apr. PMID 34085947
  2. TCF19 aggravates the malignant progression of colorectal cancer by negatively regulating WWC1. Du WB, et al. Eur Rev Med Pharmacol Sci, 2020 Jan. PMID 32016966
  3. TCF19 Promotes Cell Proliferation through Binding to the Histone H3K4me3 Mark. Mondal P, et al. Biochemistry, 2020 Feb 4. PMID 31746185
  4. TCF19 enhances cell proliferation in hepatocellular carcinoma by activating the ATK/FOXO1 signaling pathway. Zeng CX, et al. Neoplasma, 2019 Jan 15. PMID 30509085
  5. Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC. Cheung YH, et al. Hum Genet, 2011 Feb. PMID 21076979, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. TCF19 Promotes Cell Proliferation through Binding to the Histone H3K4me3 Mark.
    Title: TCF19 Promotes Cell Proliferation through Binding to the Histone H3K4me3 Mark.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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
A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients.
EBI GWAS Catalog
Common variation at 3q26.2, 6p21.33, 17p11.2 and 22q13.1 influences multiple myeloma risk.
EBI GWAS Catalog
Genome-wide association study of Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis in Europe.
EBI GWAS Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
EBI GWAS Catalog
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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

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)

  1. 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
    Q9UBH7, Q9Y242
    UniProtKB/TrEMBL
    A0A1U9X8M7
    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

  2. 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
    Q9UBH7, Q9Y242
    UniProtKB/TrEMBL
    A0A1U9X8M7
    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

  3. 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
    Q9UBH7, Q9Y242
    UniProtKB/TrEMBL
    A0A1U9X8M7
    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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    31158589..31164215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419273.1 → XP_047275229.1  transcription factor 19 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBH7
    UniProtKB/TrEMBL
    A0A1U9X8M7
    Related
    ENSP00000516544.1, ENST00000706779.1

  2. XM_047419274.1 → XP_047275230.1  transcription factor 19 isoform X1

    UniProtKB/Swiss-Prot
    Q9UBH7
    UniProtKB/TrEMBL
    A0A1U9X8M7

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    2641017..2646639
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    2417909..2423531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330342.1 → XP_054186317.1  transcription factor 19 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    2469124..2474716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330623.1 → XP_054186598.1  transcription factor 19 isoform X3

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    2502738..2508330
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330858.1 → XP_054186833.1  transcription factor 19 isoform X4

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    2416545..2422248
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331119.1 → XP_054187094.1  transcription factor 19 isoform X5

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    2461932..2467631
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331378.1 → XP_054187353.1  transcription factor 19 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31026273..31031895
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356274.1 → XP_054212249.1  transcription factor 19 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y242.2 GenPept UniProtKB/Swiss-Prot:Q9Y242

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