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TET2 tet methylcytosine dioxygenase 2 [ Homo sapiens (human) ]

Gene ID: 54790, updated on 14-Nov-2024

Summary

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Official Symbol
TET2provided by HGNC
Official Full Name
tet methylcytosine dioxygenase 2provided by HGNC
Primary source
HGNC:HGNC:25941
See related
Ensembl:ENSG00000168769 MIM:612839; AllianceGenome:HGNC:25941
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
MDS; IMD75; KIAA1546
Summary
The protein encoded by this gene is a methylcytosine dioxygenase that catalyzes the conversion of methylcytosine to 5-hydroxymethylcytosine. The encoded protein is involved in myelopoiesis, and defects in this gene have been associated with several myeloproliferative disorders. Two variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in bone marrow (RPKM 5.5), appendix (RPKM 4.6) and 25 other tissues See more
Orthologs
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Genomic context

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See TET2 in Genome Data Viewer
Location:
4q24
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (105145875..105279803)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (108456807..108590746)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (106067032..106200960)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 351, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21775 Neighboring gene nucleoporin Nup43-like Neighboring gene uncharacterized LOC124900868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21776 Neighboring gene NANOG hESC enhancer GRCh37_chr4:106064399-106064900 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21778 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:106083203-106083911 Neighboring gene TET2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21779 Neighboring gene RNA, 7SL, cytoplasmic 89, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr4:106307176-106307329 Neighboring gene inorganic pyrophosphatase 2 Neighboring gene RNA, U6 small nuclear 553, pseudogene

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 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?
  1. RNA m[5]C oxidation by TET2 regulates chromatin state and leukaemogenesis.
    Title: RNA m(5)C oxidation by TET2 regulates chromatin state and leukaemogenesis.
  2. Effects of TET2-mediated methylation reconstruction on A2058 melanoma cell sensitivity to matrix stiffness in a 3D culture system.
    Title: Effects of TET2-mediated methylation reconstruction on A2058 melanoma cell sensitivity to matrix stiffness in a 3D culture system.
  3. Organ involvement in adults with BPDCN is associated with sun exposure history, TET2 and RAS mutations, and survival.
    Title: Organ involvement in adults with BPDCN is associated with sun exposure history, TET2 and RAS mutations, and survival.
  4. NF-kappaB and TET2 promote macrophage reprogramming in hypoxia that overrides the immunosuppressive effects of the tumor microenvironment.
    Title: NF-κB and TET2 promote macrophage reprogramming in hypoxia that overrides the immunosuppressive effects of the tumor microenvironment.
  5. Hypermethylated RASAL1's promotive role in chemoresistance and tumorigenesis of choriocarcinoma was regulated by TET2 but not DNMTs.
    Title: Hypermethylated RASAL1's promotive role in chemoresistance and tumorigenesis of choriocarcinoma was regulated by TET2 but not DNMTs.
  6. Chronic TNF in the aging microenvironment exacerbates Tet2 loss-of-function myeloid expansion.
    Title: Chronic TNF in the aging microenvironment exacerbates Tet2 loss-of-function myeloid expansion.
  7. TET2 Is Downregulated in Early Esophageal Squamous Cell Carcinoma and Promotes Esophageal Squamous Cell Malignant Behaviors.
    Title: TET2 Is Downregulated in Early Esophageal Squamous Cell Carcinoma and Promotes Esophageal Squamous Cell Malignant Behaviors.
  8. [Relationship between DTA Mutations and Thromboembolism in Patients with Myeloproliferative Neoplasms].
    Title: [Relationship between DTA Mutations and Thromboembolism in Patients with Myeloproliferative Neoplasms].
  9. Uncovering the role of TET2-mediated ENPEP activation in trophoblast cell fate determination.
    Title: Uncovering the role of TET2-mediated ENPEP activation in trophoblast cell fate determination.
  10. DNA dioxygenases TET2 deficiency promotes cigarette smoke induced chronic obstructive pulmonary disease by inducing ferroptosis of lung epithelial cell.
    Title: DNA dioxygenases TET2 deficiency promotes cigarette smoke induced chronic obstructive pulmonary disease by inducing ferroptosis of lung epithelial cell.
Submit: New GeneRIF Correction See all GeneRIFs (415)

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

Associated conditions

Description Tests
Immunodeficiency 75
MedGen: C5436860 OMIM: 619126 GeneReviews: Not available
not available
Myelodysplastic syndrome
MedGen: C3463824 OMIM: 614286 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
A genome-wide association study of host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed.
EBI GWAS Catalog
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog
Identification of a melanoma susceptibility locus and somatic mutation in TET2.
EBI GWAS Catalog
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
EBI GWAS Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20032, KIAA1546, MGC125715

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5-methylcytosine dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5-methylcytosine dioxygenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 5-methylcytosine dioxygenase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables 5-methylcytosine dioxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables ferrous iron binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromosomal 5-methylcytosine DNA demethylation, oxidation pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in leukocyte differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in myeloid cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in myeloid cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of gene expression via chromosomal CpG island demethylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein O-linked glycosylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein O-linked glycosylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
methylcytosine dioxygenase TET2
Names
probable methylcytosine dioxygenase TET2
ten-eleven translocation 2
tet oncogene family member 2
NP_001120680.1
NP_060098.3
XP_005263139.1
XP_006714305.1
XP_016863808.1
XP_024309870.1
XP_024309871.1
XP_047271795.1
XP_047271796.1
XP_047271797.1
XP_047271798.1
XP_047271799.1
XP_054206247.1
XP_054206248.1
XP_054206249.1
XP_054206250.1
XP_054206251.1
XP_054206252.1
XP_054206253.1
XP_054206254.1
XP_054206255.1
XP_054206256.1

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.

Genomic

  1. NG_028191.1 RefSeqGene

    Range
    5001..138929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_626

mRNA and Protein(s)

  1. NM_001127208.3 → NP_001120680.1  methylcytosine dioxygenase TET2 isoform a

    See identical proteins and their annotated locations for NP_001120680.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC004069, AC026029
    Consensus CDS
    CCDS47120.1
    UniProtKB/Swiss-Prot
    B5MDU0, Q2TB88, Q3LIB8, Q6N021, Q96JX5, Q9HCM6, Q9NXW0
    UniProtKB/TrEMBL
    A0A158SIU0, E7EQS8
    Related
    ENSP00000369351.4, ENST00000380013.9
    Conserved Domains (1) summary
    pfam12851
    Location:1290 → 1417
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  2. NM_017628.4 → NP_060098.3  methylcytosine dioxygenase TET2 isoform b

    See identical proteins and their annotated locations for NP_060098.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC026029, BX640738
    Consensus CDS
    CCDS3666.1
    UniProtKB/TrEMBL
    E7EPB1
    Related
    ENSP00000306705.2, ENST00000305737.6

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    105145875..105279803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024454103.2 → XP_024309871.1  methylcytosine dioxygenase TET2 isoform X1

    UniProtKB/Swiss-Prot
    B5MDU0, Q2TB88, Q3LIB8, Q6N021, Q96JX5, Q9HCM6, Q9NXW0
    UniProtKB/TrEMBL
    A0A158SIU0, E7EQS8
    Conserved Domains (1) summary
    pfam12851
    Location:1290 → 1417
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  2. XM_024454102.2 → XP_024309870.1  methylcytosine dioxygenase TET2 isoform X1

    UniProtKB/Swiss-Prot
    B5MDU0, Q2TB88, Q3LIB8, Q6N021, Q96JX5, Q9HCM6, Q9NXW0
    UniProtKB/TrEMBL
    A0A158SIU0, E7EQS8
    Conserved Domains (1) summary
    pfam12851
    Location:1290 → 1417
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  3. XM_006714242.4 → XP_006714305.1  methylcytosine dioxygenase TET2 isoform X2

    UniProtKB/TrEMBL
    E7EQS8
    Conserved Domains (1) summary
    pfam12851
    Location:1190 → 1317
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  4. XM_005263082.4 → XP_005263139.1  methylcytosine dioxygenase TET2 isoform X1

    See identical proteins and their annotated locations for XP_005263139.1

    UniProtKB/Swiss-Prot
    B5MDU0, Q2TB88, Q3LIB8, Q6N021, Q96JX5, Q9HCM6, Q9NXW0
    UniProtKB/TrEMBL
    A0A158SIU0, E7EQS8
    Conserved Domains (1) summary
    pfam12851
    Location:1290 → 1417
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  5. XM_047415839.1 → XP_047271795.1  methylcytosine dioxygenase TET2 isoform X3

  6. XM_047415840.1 → XP_047271796.1  methylcytosine dioxygenase TET2 isoform X4

  7. XM_047415841.1 → XP_047271797.1  methylcytosine dioxygenase TET2 isoform X5

    Related
    ENSP00000265149.5, ENST00000265149.9

  8. XM_047415842.1 → XP_047271798.1  methylcytosine dioxygenase TET2 isoform X6

  9. XM_017008319.2 → XP_016863808.1  methylcytosine dioxygenase TET2 isoform X6

    UniProtKB/TrEMBL
    E7EPB1

  10. XM_047415843.1 → XP_047271799.1  methylcytosine dioxygenase TET2 isoform X6

RNA

  1. XR_007057933.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    108456807..108590746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350273.1 → XP_054206248.1  methylcytosine dioxygenase TET2 isoform X1

  2. XM_054350274.1 → XP_054206249.1  methylcytosine dioxygenase TET2 isoform X1

  3. XM_054350275.1 → XP_054206250.1  methylcytosine dioxygenase TET2 isoform X2

  4. XM_054350272.1 → XP_054206247.1  methylcytosine dioxygenase TET2 isoform X1

  5. XM_054350276.1 → XP_054206251.1  methylcytosine dioxygenase TET2 isoform X3

  6. XM_054350277.1 → XP_054206252.1  methylcytosine dioxygenase TET2 isoform X4

  7. XM_054350278.1 → XP_054206253.1  methylcytosine dioxygenase TET2 isoform X5

  8. XM_054350280.1 → XP_054206255.1  methylcytosine dioxygenase TET2 isoform X6

  9. XM_054350279.1 → XP_054206254.1  methylcytosine dioxygenase TET2 isoform X6

  10. XM_054350281.1 → XP_054206256.1  methylcytosine dioxygenase TET2 isoform X6

RNA

  1. XR_008486995.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6N021.3 GenPept UniProtKB/Swiss-Prot:Q6N021

Gene LinkOut

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