Gene Gene information from NCBI Gene database.
Entrez ID 6929
Gene name Transcription factor 3
Gene symbol TCF3
Synonyms (NCBI Gene)
AGM8AGM8AAGM8BE2AE47ITF1TCF-3VDIRbHLHb21p75
Chromosome 19
Chromosome location 19p13.3
Summary This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodi
SNPs SNP information provided by dbSNP.
2
SNP ID Visualize variation Clinical significance Consequence
rs879255271 C>T Pathogenic Downstream transcript variant, missense variant, intron variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs1599413207 C>T Likely-pathogenic Downstream transcript variant, genic downstream transcript variant, non coding transcript variant, coding sequence variant, missense variant, intron variant
miRNA miRNA information provided by mirtarbase database.
384
miRTarBase ID miRNA Experiments Reference
MIRT007321 hsa-miR-17-5p Luciferase reporter assay 23492770
MIRT007321 hsa-miR-17-5p Luciferase reporter assay 23492770
MIRT007321 hsa-miR-17-5p Luciferase reporter assay 23492770
MIRT023195 hsa-miR-124-3p Microarray 18668037
MIRT044472 hsa-miR-320a CLASH 23622248
Transcription factors Transcription factors information provided by TRRUST V2 database.
5
Transcription factor Regulation Reference
FIGLA Unknown 18499083
ID3 Repression 24492847
LDB1 Repression 10767331
LEF1 Unknown 8479911
LMX1B Activation 10767331
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
63
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 14576336
GO:0000785 Component Chromatin IBA
GO:0000785 Component Chromatin IDA 21828274
GO:0000785 Component Chromatin ISA
GO:0000791 Component Euchromatin IDA 10652346
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
147141 11633 ENSG00000071564
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P15923
Protein name Transcription factor E2-alpha (Class B basic helix-loop-helix protein 21) (bHLHb21) (Immunoglobulin enhancer-binding factor E12/E47) (Immunoglobulin transcription factor 1) (Kappa-E2-binding factor) (Transcription factor 3) (TCF-3) (Transcription factor I
Protein function Transcriptional regulator involved in the initiation of neuronal differentiation and mesenchymal to epithelial transition (By similarity). Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in d
PDB 2MH0 , 2YPA , 2YPB , 3U5V , 6MGN
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00010 HLH 550 603 Helix-loop-helix DNA-binding domain Domain
Sequence
MNQPQRMAPVGTDKELSDLLDFSMMFPLPVTNGKGRPASLAGAQFGGSGLEDRPSSGSWG
SGDQSSSSFDPSRTFSEGTHFTESHSSLSSSTFLGPGLGGKSGERGAYASFGRDAGVGGL
TQAGFLSGELALNSPGPLSPSGMKGTSQYYPSYSGSSRRRAADGSLDTQPKKVRKVPPGL
PSSVYPPSSGEDYGRDATAYPSAKTPSSTYPAPFYVADGSLHPSAELWSPPGQAGFGPML
GGGSSPLPLPPGSGPVGSSGSSSTFGGLHQHERMGYQLHGAEVNGGLPSASSFSSAPGAT
YGGVSSHTPPVSGADSLLGSRGTTAGSSGDALGKALASIYSPDHSSNNFSSSPSTPVGSP
QGLAGTSQWPRAGAPGALSPSYDGGLHGLQSKIEDHLDEAIHVLRSHAVGTAGDMHTLLP
GHGALASGFTGPMSLGGRHAGLVGGSHPEDGLAGSTSLMHNHAALPSQPGTLPDLSRPPD
SYSGLGRAGATAAASEIKREEKEDEENTSAADHSEEEKKELKAPRARTSPDEDEDDLLPP
EQKAEREKERRVANNARERLRVRDINEAFKELGRMCQLHLNSEKPQTKLLILHQAVSVIL
NLE
QQVRERNLNPKAACLKRREEEKVSGVVGDPQMVLSAPHPGLSEAHNPAGHM
Sequence length 654
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Signaling pathways regulating pluripotency of stem cells
Human T-cell leukemia virus 1 infection
Transcriptional misregulation in cancer
  Myogenesis
RUNX1 regulates transcription of genes involved in differentiation of HSCs
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
40
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Agammaglobulinemia 8, autosomal dominant Pathogenic rs879255271, rs2061880735 RCV000211091
RCV001262287
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Agammaglobulinemia 8b, autosomal recessive Pathogenic rs2146131822 RCV002221970
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Multiple myeloma Likely pathogenic rs1599413207 RCV000984089
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Uncertain significance; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTOSOMAL AGAMMAGLOBULINEMIA ClinGen, GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute leukemia Leukemia BEFREE 16173964, 1999956
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 1348433, 1516826, 15543624, 17311319, 18024406, 19587702, 21732038, 2243503, 23181981, 24578304, 24990612, 25116187, 25273558, 25551271, 25780007
View all (7 more)
★☆☆☆☆
Found in Text Mining only
Acute pancreatitis Pancreatitis BEFREE 29018453
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of prostate Prostate adenocarcinoma BEFREE 15948150
★☆☆☆☆
Found in Text Mining only
Adult Acute Lymphocytic Leukemia Lymphocytic Leukemia BEFREE 1348433, 15543624, 25116187, 26214592, 30510082
★☆☆☆☆
Found in Text Mining only
Adult Hodgkin Lymphoma Hodgkin Lymphoma BEFREE 24920014
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 17550129
★☆☆☆☆
Found in Text Mining only
African Burkitt`s lymphoma African Burkitt`s Lymphoma CTD_human_DG 17244677, 1967982
★☆☆☆☆
Found in Text Mining only
Agammaglobulinemia Agammaglobulinemia Pubtator 24216514 Associate
★☆☆☆☆
Found in Text Mining only
Agammaglobulinemia Agammaglobulinemia GENOMICS_ENGLAND_DG 29114388
★☆☆☆☆
Found in Text Mining only