TFEC

gene
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Also known as TCFECTFECLbHLHe34

Summary

TFEC (transcription factor EC, HGNC:11754) is a protein-coding gene on chromosome 7q31.2, encoding Transcription factor EC (O14948). Transcriptional regulator that acts as a repressor or an activator.

This gene encodes a member of the micropthalmia (MiT) family of basic helix-loop-helix leucine zipper transcription factors. MiT transcription factors regulate the expression of target genes by binding to E-box recognition sequences as homo- or heterodimers, and play roles in multiple cellular processes including survival, growth and differentiation. The encoded protein is a transcriptional activator of the nonmuscle myosin II heavy chain-A gene, and may also co-regulate target genes in osteoclasts as a heterodimer with micropthalmia-associated transcription factor. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 22797 — RefSeq curated summary.

At a glance

  • GWAS associations: 20
  • Clinical variants (ClinVar): 53 total
  • MANE Select transcript: NM_012252

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11754
Approved symbolTFEC
Nametranscription factor EC
Location7q31.2
Locus typegene with protein product
StatusApproved
AliasesTCFEC, TFECL, bHLHe34
Ensembl geneENSG00000105967
Ensembl biotypeprotein_coding
OMIM604732
Entrez22797

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 9 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000265440, ENST00000320239, ENST00000393485, ENST00000457268, ENST00000462828, ENST00000465322, ENST00000474337, ENST00000484212, ENST00000497829, ENST00000871198, ENST00000871199, ENST00000871200, ENST00000952248

RefSeq mRNA: 3 — MANE Select: NM_012252 NM_001018058, NM_001244583, NM_012252

CCDS: CCDS34738, CCDS5762, CCDS59076

Canonical transcript exons

ENST00000265440 — 8 exons

ExonStartEnd
ENSE00000881885115974170115974256
ENSE00001015841116030633116030763
ENSE00001015842115956679115956793
ENSE00001015845115950874115950949
ENSE00001015847115954586115954642
ENSE00003564412115984262115984513
ENSE00003659572115941893115942040
ENSE00003847030115935152115940931

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 95.47.

FANTOM5 (CAGE): breadth broad, TPM avg 14.5948 / max 885.0494, expressed in 473 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
8580213.4467446
858010.6061173
858090.2261101
858080.114057
857980.107615
857970.094317

Top tissues by expression

282 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
monocyteCL:000057695.47gold quality
mononuclear cellCL:000084295.11gold quality
leukocyteCL:000073894.34gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.10gold quality
granulocyteCL:000009485.45gold quality
vermiform appendixUBERON:000115485.25gold quality
nephron tubuleUBERON:000123183.34gold quality
bone marrow cellCL:000209282.98gold quality
spleenUBERON:000210680.76gold quality
lymph nodeUBERON:000002980.70gold quality
bone marrowUBERON:000237180.14gold quality
jejunal mucosaUBERON:000039979.58gold quality
upper lobe of left lungUBERON:000895279.14gold quality
upper lobe of lungUBERON:000894879.05gold quality
right lungUBERON:000216778.81gold quality
caecumUBERON:000115377.49gold quality
calcaneal tendonUBERON:000370177.18gold quality
kidney epitheliumUBERON:000481976.87gold quality
small intestine Peyer’s patchUBERON:000345476.31gold quality
gall bladderUBERON:000211074.86gold quality
adult mammalian kidneyUBERON:000008274.80gold quality
rectumUBERON:000105274.67gold quality
bloodUBERON:000017874.64gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099174.13gold quality
small intestineUBERON:000210873.97gold quality
lungUBERON:000204873.85gold quality
renal glomerulusUBERON:000007473.74gold quality
metanephric glomerulusUBERON:000473673.70gold quality
kidneyUBERON:000211373.63gold quality
cortex of kidneyUBERON:000122573.54gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes11.92

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

TargetRegulation
ACP5
CD40
HMOX1Unknown
MYH9Activation

JASPAR motifs

MotifNameFamily
MA0871.1TFECbHLH-ZIP
MA0871.2TFECbHLH-ZIP
MA0871.3TFECbHLH-ZIP

JASPAR matrix evidence (PMIDs): PMID:15186484

Upstream regulators (CollecTRI, top): ETS2, ETV7, PAX6, SPI1

miRNA regulators (miRDB)

215 targeting TFEC, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-3646100.0073.565283
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3924100.0072.092394
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-4262100.0073.263931
HSA-MIR-340-5P100.0072.504437
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-428299.9975.366408
HSA-MIR-453199.9969.703181

Literature-anchored findings (GeneRIF, showing 1)

  • Two alternatively spliced TFEC isoforms have been found to be sequence-specific transcriptional activators of the nonmuscle myosin II heavy chain-A gene in transfected cells. (PMID:11467950)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotfecENSDARG00000098745
mus_musculusTfecENSMUSG00000029553
rattus_norvegicusTfecENSRNOG00000061595
drosophila_melanogasterMitfFBGN0263112
caenorhabditis_elegansWBGENE00020930

Paralogs (3): TFE3 (ENSG00000068323), TFEB (ENSG00000112561), MITF (ENSG00000187098)

Protein

Protein identifiers

Transcription factor ECO14948 (reviewed: O14948)

Alternative names: Class E basic helix-loop-helix protein 34, Transcription factor EC-like

All UniProt accessions (2): O14948, B7Z757

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional regulator that acts as a repressor or an activator. Acts as a transcriptional repressor on minimal promoter containing element F (that includes an E-box sequence). Binds to element F in an E-box sequence-specific manner. Acts as a transcriptional transactivator on the proximal promoter region of the tartrate-resistant acid phosphatase (TRAP) E-box containing promoter. Collaborates with MITF in target gene activation. Acts as a transcriptional repressor on minimal promoter containing mu E3 enhancer sequence. Binds to mu E3 DNA sequence of the immunoglobulin heavy-chain gene enhancer. Binds DNA in a homo- or heterodimeric form.

Subunit / interactions. Homodimer. Forms heterodimers with TFE3. Forms heterodimers with MITF. Interacts with MITF.

Subcellular location. Nucleus.

Tissue specificity. Expressed moderately in spleen, kidney, bone marrow, small intestine and leukocytes. Expressed weakly in testis, trachea and colon.

Similarity. Belongs to the MiT/TFE family.

Isoforms (4)

UniProt IDNamesCanonical?
O14948-11, TFEC-l, TFECLyes
O14948-22, TFEC-s
O14948-33
O14948-44, TFEC-C

RefSeq proteins (3): NP_001018068, NP_001231512, NP_036384* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011598bHLH_domDomain
IPR021802MiT/TFE_CDomain
IPR036638HLH_DNA-bd_sfHomologous_superfamily

Pfam: PF00010, PF11851

UniProt features (14 total): splice variant 5, sequence variant 3, region of interest 3, chain 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O14948-F163.790.30

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-9856649Transcriptional and post-translational regulation of MITF-M expression and activity
R-HSA-1266738Developmental Biology
R-HSA-9730414MITF-M-regulated melanocyte development

MSigDB gene sets: 286 (showing top): BROWNE_HCMV_INFECTION_4HR_UP, TAATAAT_MIR126, WALLACE_PROSTATE_CANCER_RACE_UP, LANG_MYB_FAMILY_TARGETS, HNF1_Q6, FOXD3_01, BLALOCK_ALZHEIMERS_DISEASE_UP, CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP, ACATTCC_MIR1_MIR206, GGGNNTTTCC_NFKB_Q6_01, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, GOBP_CELLULAR_RESPONSE_TO_HEAT, GATA1_04, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, NRF2_Q4

GO Biological Process (5): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), cellular response to heat (GO:0034605), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), protein dimerization activity (GO:0046983), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
MITF-M-regulated melanocyte development1
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding4
regulation of transcription by RNA polymerase II3
transcription by RNA polymerase II3
cellular anatomical structure3
DNA-binding transcription factor activity, RNA polymerase II-specific2
negative regulation of DNA-templated transcription1
regulation of DNA-templated transcription1
response to heat1
cellular response to stress1
positive regulation of DNA-templated transcription1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription repressor activity1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
protein binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1
cytoplasm1

Protein interactions and networks

STRING

1446 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TFECCTSKP43235720
TFECTFE3P19532622
TFECTYRP14679579
TFECMITFO75030559
TFECDCTP40126555
TFECHMOX1P09601533
TFECASPSCR1Q9BZE9525
TFECPRCCQ92733513
TFECGPR143P51810507
TFECTYRP1P17643487
TFECSOX10P56693487
TFECGPNMBQ14956454
TFECPAX3P23760433
TFECDIAPH1O60610429
TFECMAFBQ9Y5Q3406

IntAct

13 interactions, top by confidence:

ABTypeScore
TFECNAPBpsi-mi:“MI:0915”(physical association)0.560
DEFB127TFECpsi-mi:“MI:0915”(physical association)0.560
NAPBTFECpsi-mi:“MI:0915”(physical association)0.560
TFECDEFB127psi-mi:“MI:0915”(physical association)0.560
TFECpsi-mi:“MI:0915”(physical association)0.370
XCL1TFECpsi-mi:“MI:0915”(physical association)0.370
DCKTFECpsi-mi:“MI:0915”(physical association)0.370
HNRNPA1TFECpsi-mi:“MI:0915”(physical association)0.370
ZMAT2TFECpsi-mi:“MI:0915”(physical association)0.370
TFEBTFECpsi-mi:“MI:0914”(association)0.350

BioGRID (17): NAPB (Two-hybrid), DEFB127 (Two-hybrid), TFEC (Affinity Capture-MS), TFEC (Proximity Label-MS), SMCO4 (Two-hybrid), LPAR3 (Two-hybrid), TFEC (Two-hybrid), TET2 (Affinity Capture-Western), TFEC (Positive Genetic), TFEC (Reconstituted Complex), TFE3 (Reconstituted Complex), TFEC (Affinity Capture-MS), TFEC (Affinity Capture-Western), TFEC (Affinity Capture-RNA), TFEC (Two-hybrid)

ESM2 similar proteins: A0A0A7HJC7, A0A0B2XG51, A0A0F0IP79, A1DG01, A2R6G8, A2T713, A2T7L8, B0XYJ1, B2AR36, B2W978, B8NLU5, B8NNN3, C0STD9, C7YM38, E9EMI7, E9EPV1, E9ES99, E9RD40, G4N2B2, G5ECU7, I1S0E2, I1S4T3, K9FWK0, O14948, O16850, O74252, P22022, P38165, Q00096, Q01870, Q09926, Q0U7C8, Q152V3, Q1XGE2, Q2GSA4, Q2U616, Q2UMT9, Q2UUM2, Q4W9W8, Q4WEY8

Diamond homologs: A0A286LEZ9, A2T713, A2T7L8, A4IFU7, O02818, O14948, O75030, O88368, P0DPB0, P17106, P19484, P19532, P22415, P49379, Q05B92, Q07957, Q08874, Q10186, Q5A1E3, Q5XFQ6, Q61069, Q63302, Q64092, Q6XBT4, Q9R210, Q9WTW4, H2KZZ2, P38165, A3KNA7, O43019, O97676, P36956, P56720, Q12772, Q3T1I5, Q3U1N2, Q4WIN1, Q59RL7, Q60416, Q60429

SIGNOR signaling

1 interactions.

AEffectBMechanism
TFEC“up-regulates quantity by expression”MYH9“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

53 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign1
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1571 predictions. Top by Δscore:

VariantEffectΔscore
7:115941920:AG:Adonor_gain1.0000
7:115950872:A:ACdonor_gain1.0000
7:115950873:C:CCdonor_gain1.0000
7:115954584:A:ACdonor_gain1.0000
7:115954585:C:CCdonor_gain1.0000
7:115954648:C:CTacceptor_gain1.0000
7:115956673:CATTA:Cdonor_loss1.0000
7:115956674:ATTAC:Adonor_loss1.0000
7:115956675:TTACC:Tdonor_loss1.0000
7:115956676:TAC:Tdonor_loss1.0000
7:115956677:AC:Adonor_loss1.0000
7:115956678:C:Adonor_loss1.0000
7:115956789:GATAA:Gacceptor_gain1.0000
7:115956790:ATAA:Aacceptor_gain1.0000
7:115956791:TAA:Tacceptor_gain1.0000
7:115956792:AA:Aacceptor_gain1.0000
7:115956794:C:CCacceptor_gain1.0000
7:115956794:CTT:Cacceptor_loss1.0000
7:115956795:T:Cacceptor_gain1.0000
7:115956795:T:TCacceptor_gain1.0000
7:115974169:CTGTT:Cdonor_gain1.0000
7:115942041:C:CCacceptor_gain0.9900
7:115950873:CGGAT:Cdonor_gain0.9900
7:115950950:C:CCacceptor_gain0.9900
7:115954643:C:CCacceptor_gain0.9900
7:115954649:A:Tacceptor_gain0.9900
7:115974168:A:ACdonor_gain0.9900
7:115974169:C:CCdonor_gain0.9900
7:115984261:CATG:Cdonor_gain0.9900
7:115984264:G:Adonor_gain0.9900

AlphaMissense

2278 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:115942011:A:GL182P1.000
7:115942022:T:AK178N1.000
7:115942022:T:GK178N1.000
7:115942023:T:AK178I1.000
7:115942024:T:GK178Q1.000
7:115950936:T:AR151S1.000
7:115950936:T:GR151S1.000
7:115950937:C:GR151T1.000
7:115941981:A:GL192P0.999
7:115942011:A:TL182Q0.999
7:115942024:T:CK178E0.999
7:115950913:A:CI159S0.999
7:115950913:A:GI159T0.999
7:115950925:A:CI155S0.999
7:115950933:C:AR152S0.999
7:115950933:C:GR152S0.999
7:115950934:C:AR152M0.999
7:115950942:T:AR149S0.999
7:115950942:T:GR149S0.999
7:115950945:T:AE148D0.999
7:115950945:T:GE148D0.999
7:115954595:G:CH144D0.999
7:115940927:A:GL223P0.998
7:115942006:C:GA184P0.998
7:115942021:C:GG179R0.998
7:115942021:C:TG179R0.998
7:115950904:A:GL162P0.998
7:115950913:A:TI159N0.998
7:115950916:C:GR158P0.998
7:115950921:A:CN156K0.998

dbSNP variants (sampled 300 via entrez): RS1000019732 (7:116029819 G>C), RS1000025190 (7:116054526 G>A), RS1000043038 (7:116006142 G>A), RS1000051500 (7:116132082 C>A,T), RS1000051964 (7:116088215 A>G,T), RS1000074305 (7:116006239 T>C), RS1000097322 (7:115941531 A>G), RS1000100630 (7:116047476 C>A), RS1000102348 (7:115965023 A>G), RS1000102955 (7:115937124 T>C), RS1000120670 (7:116022772 A>G), RS1000131745 (7:115983364 A>T), RS1000147327 (7:116102606 T>A,C), RS1000176836 (7:116018695 G>A), RS1000178840 (7:116102855 C>T)

Disease associations

OMIM: gene MIM:604732 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

20 associations (top):

StudyTraitp-value
GCST003995_22Tonsillectomy8.000000e-10
GCST004904_58Body mass index9.000000e-09
GCST005014_127Tonsillectomy8.000000e-10
GCST005170_3Intraocular pressure2.000000e-20
GCST005580_287Intraocular pressure1.000000e-09
GCST006412_69Intraocular pressure1.000000e-16
GCST007325_203General risk tolerance (MTAG)2.000000e-08
GCST007325_205General risk tolerance (MTAG)2.000000e-08
GCST007325_250General risk tolerance (MTAG)2.000000e-09
GCST007325_47General risk tolerance (MTAG)5.000000e-08
GCST007326_75Number of sexual partners1.000000e-08
GCST007576_200Chronotype8.000000e-09
GCST008163_232Height5.000000e-07
GCST010916_15Proportion of activated microglia (inferior temporal cortex)7.000000e-07
GCST012292_12Schizophrenia, bipolar disorder or recurrent major depressive disorder x sex interaction8.000000e-06
GCST012297_3Schizophrenia, bipolar disorder or major depressive disorder9.000000e-06
GCST012298_11Schizophrenia, bipolar disorder or major depressive disorder x sex interaction6.000000e-06
GCST012489_140Heel bone mineral density x serum urate levels interaction2.000000e-08
GCST90002400_47Plateletcrit4.000000e-10
GCST90002401_465Platelet distribution width3.000000e-09

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0007924tonsillectomy risk measurement
EFO:0004340body mass index
EFO:0004695intraocular pressure measurement
EFO:0008579risk-taking behaviour
EFO:0008328chronotype measurement
EFO:0004952disease recurrence
EFO:0008343sex interaction measurement
EFO:0004531urate measurement
EFO:0009270heel bone mineral density
EFO:0007985platelet crit
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Nickeldecreases expression, increases expression3
Ethyl Methanesulfonatedecreases expression, increases expression2
Methyl Methanesulfonatedecreases expression, increases expression2
propionaldehydedecreases expression1
bisphenol Aincreases methylation1
o,p’-DDTincreases expression1
butyraldehydedecreases expression1
pentanaldecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
bisphenol Sincreases methylation1
NSC 689534affects binding, increases expression1
Resveratrolaffects cotreatment, increases expression1
Air Pollutants, Occupationaldecreases expression1
Aldehydesdecreases expression1
Amphotericin Bdecreases expression1
Cisplatindecreases expression1
Copperaffects binding, increases expression1
Etoposidedecreases expression1
Golddecreases expression1
Hydroxyureadecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Rifampinincreases expression1
Silicon Dioxideincreases expression1
Tretinoinincreases expression1
Aflatoxin M1decreases expression1
Mitomycindecreases expression1
Antirheumatic Agentsdecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): major depressive disorder