FRAT1

gene
On this page

Summary

FRAT1 (FRAT regulator of Wnt signaling pathway 1, HGNC:3944) is a protein-coding gene on chromosome 10q24.1, encoding Proto-oncogene FRAT1 (Q92837). Positively regulates the Wnt signaling pathway by stabilizing beta-catenin through the association with GSK-3.

The protein encoded by this gene belongs to the GSK-3-binding protein family. The protein inhibits GSK-3-mediated phosphorylation of beta-catenin and positively regulates the Wnt signaling pathway. It may function in tumor progression and in lymphomagenesis.

Source: NCBI Gene 10023 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 49 total
  • MANE Select transcript: NM_005479

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3944
Approved symbolFRAT1
NameFRAT regulator of Wnt signaling pathway 1
Location10q24.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000165879
Ensembl biotypeprotein_coding
OMIM602503
Entrez10023

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000371021, ENST00000490980

RefSeq mRNA: 1 — MANE Select: NM_005479 NM_005479

CCDS: CCDS7455

Canonical transcript exons

ENST00000371021 — 1 exons

ExonStartEnd
ENSE000014541389731927197321915

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 92.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.6294 / max 208.2473, expressed in 1235 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1064242.6626853
1064251.9668705

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bloodUBERON:000017892.49gold quality
monocyteCL:000057691.48gold quality
mononuclear cellCL:000084291.18gold quality
leukocyteCL:000073891.13gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.66gold quality
granulocyteCL:000009487.10gold quality
pancreatic ductal cellCL:000207985.97gold quality
secondary oocyteCL:000065584.50gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.84gold quality
oocyteCL:000002382.14gold quality
right lobe of liverUBERON:000111480.27gold quality
bone marrowUBERON:000237179.25gold quality
spleenUBERON:000210679.16gold quality
mucosa of transverse colonUBERON:000499177.61gold quality
palpebral conjunctivaUBERON:000181277.36gold quality
bone marrow cellCL:000209277.23gold quality
apex of heartUBERON:000209875.67gold quality
right testisUBERON:000453475.54gold quality
left testisUBERON:000453375.22gold quality
liverUBERON:000210774.11gold quality
endothelial cellCL:000011573.50silver quality
testisUBERON:000047372.96gold quality
hindlimb stylopod muscleUBERON:000425272.88gold quality
stromal cell of endometriumCL:000225572.70gold quality
vermiform appendixUBERON:000115471.96gold quality
trabecular bone tissueUBERON:000248371.58gold quality
duodenumUBERON:000211471.48gold quality
olfactory segment of nasal mucosaUBERON:000538671.37gold quality
right lungUBERON:000216771.33gold quality
body of stomachUBERON:000116170.62gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting FRAT1, 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-4668-3P100.0068.742635
HSA-MIR-3163100.0077.238605
HSA-MIR-548AW99.9972.573559
HSA-MIR-118499.9968.191458
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-129799.9173.413162
HSA-MIR-345-3P99.8970.231421
HSA-MIR-391999.8769.452489
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-205-5P99.8170.051557
HSA-MIR-26A-5P99.7873.522303
HSA-MIR-26B-5P99.7873.512305
HSA-MIR-446599.7172.562096
HSA-MIR-518A-5P99.7069.012209
HSA-MIR-52799.7069.012209
HSA-MIR-472999.6972.184233
HSA-MIR-4690-5P99.6566.24813
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084

Literature-anchored findings (GeneRIF, showing 18)

  • CKI epsilon-dependent phosphorylation of Dvl enhances the formation of a complex of Dvl-1 with Frat-1 and this complex leads to the activation of Wnt-3a-induced accumulation of beta-catenin (PMID:12556519)
  • findings support that Wnt/beta-catenin signalling may be aberrantly activated through FRAT1 overexpression in ovarian serous adenocarcinomas (PMID:16479254)
  • PKA phosphorylates FRAT1 in vitro as well as in intact cells and may play a role in regulating the inhibitory activity of FRAT1 toward GSK-3. (PMID:16982607)
  • Aberrant activation of beta-catenin/TCF pathway in esophageal cancer appears to be due to upstream events such as FRAT1 overexpression, and c-Myc may be an important element in oncogenesis of human ESCC induced by FRAT1. (PMID:18498136)
  • Elevated expression of FRAT1 was associated with astrocytomas. (PMID:20041315)
  • Our results suggest that FRAT1 may be an important factor in the tumorigenesis and progression of gliomas, and could be used as a potential molecular marker for pathological diagnosis and a target for biological therapy. (PMID:20096670)
  • Down-regulation of Frat1 expression reduced invasive ability in A549 cell line, further supporting idea that Frat1 may play crucial role in carcinogenesis, tumor invasiveness and dissemination in human lung cancer. (PMID:21818639)
  • The overexpression of Frat1 and beta-catenin was correlated with tumor differentiation, TNM stage, lymph node metastasis, and poor prognosis of NSCLC. (PMID:22528942)
  • These results highlight the potential role of FRAT1 in tumorigenesis and progression of glioblastoma. (PMID:23613813)
  • The mechanism of inhibiting beta-catenin phosphorylation involves the NDRG1-mediated upregulation of the GSK3beta-binding protein FRAT1. (PMID:24829151)
  • Positive ROR2 and FRAT1 expression is associated with the progression and poor prognosis of chondrosarcoma. (PMID:25387569)
  • FRAT1 overexpression correlates with pathologic grade, proliferation, invasion and angiogenesis in brain gliomas. (PMID:25922553)
  • FRAT1 and ABCG2 overexpression is associated with carcinogenesis, progression, and poor prognosis in patients with Pancreatic ductal adenocarcinoma. (PMID:26178481)
  • The results of the present study suggest that nuclear FRAT1 activates the Wnt/beta-catenin signaling pathway and confers an increase in prostate cancer cell growth. (PMID:27599661)
  • These data suggest a potential role for targeting FRAT1 in the prevention of hypoxia-induced HCC cancer progression and metastasis mediated by epithelial-to-mesenchymal transition (PMID:27666874)
  • LncRNA CCAT1 promotes prostate cancer cells proliferation, migration, and invasion through regulation of miR-490-3p/FRAT1 axis. (PMID:34319909)
  • FRAT1 promotes the angiogenic properties of human glioblastoma cells via VEGFA. (PMID:35059733)
  • The miR-3648/FRAT1-FRAT2/c-Myc negative feedback loop modulates the metastasis and invasion of gastric cancer cells. (PMID:36153370)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusFrat1ENSMUSG00000067199
mus_musculusPeg12ENSMUSG00000070526
rattus_norvegicusPeg12ENSRNOG00000024429
rattus_norvegicusFrat1ENSRNOG00000067076

Paralogs (1): FRAT2 (ENSG00000181274)

Protein

Protein identifiers

Proto-oncogene FRAT1Q92837 (reviewed: Q92837)

Alternative names: Frequently rearranged in advanced T-cell lymphomas 1

All UniProt accessions (1): Q92837

UniProt curated annotations — full annotation on UniProt →

Function. Positively regulates the Wnt signaling pathway by stabilizing beta-catenin through the association with GSK-3. May play a role in tumor progression and collaborate with PIM1 and MYC in lymphomagenesis.

Subunit / interactions. Binds DVL1. Binds GSK-3 and prevent GSK-3-dependent phosphorylation.

Subcellular location. Cytoplasm.

Post-translational modifications. Phosphorylated.

Similarity. Belongs to the GSK-3-binding protein family.

RefSeq proteins (1): NP_005470* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008014GSK3-bdFamily

Pfam: PF05350

UniProt features (14 total): region of interest 5, modified residue 3, sequence conflict 2, helix 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

6 structures.

PDBMethodResolution (Å)
4AFJX-RAY DIFFRACTION1.98
3ZRKX-RAY DIFFRACTION2.37
3ZRLX-RAY DIFFRACTION2.48
3ZRMX-RAY DIFFRACTION2.49
1GNGX-RAY DIFFRACTION2.6
5OY4X-RAY DIFFRACTION3.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92837-F160.810.12

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 88, 249, 252

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-196299Beta-catenin phosphorylation cascade
R-HSA-4641262Disassembly of the destruction complex and recruitment of AXIN to the membrane

MSigDB gene sets: 237 (showing top): BENPORATH_ES_WITH_H3K27ME3, YANG_BREAST_CANCER_ESR1_LASER_UP, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_REGULATION_OF_PROTEIN_EXPORT_FROM_NUCLEUS, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_NUCLEAR_TRANSPORT, GOBP_REGULATION_OF_NUCLEOCYTOPLASMIC_TRANSPORT, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_REGULATION_OF_CELLULAR_LOCALIZATION, BILD_E2F3_ONCOGENIC_SIGNATURE, GOBP_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GNF2_HCK, TCCAGAT_MIR5165P

GO Biological Process (4): regulation of protein export from nucleus (GO:0046825), canonical Wnt signaling pathway (GO:0060070), positive regulation of canonical Wnt signaling pathway (GO:0090263), Wnt signaling pathway (GO:0016055)

GO Molecular Function (2): molecular function inhibitor activity (GO:0140678), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Degradation of beta-catenin by the destruction complex1
TCF dependent signaling in response to WNT1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
protein export from nucleus1
regulation of intracellular protein transport1
regulation of nucleocytoplasmic transport1
Wnt signaling pathway1
positive regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
regulation of canonical Wnt signaling pathway1
cell surface receptor signaling pathway1
molecular function regulator activity1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

576 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FRAT1AXIN1O15169984
FRAT1GSK3BP49841979
FRAT1DVL1O14640954
FRAT1RHOAP06749769
FRAT1CTNNB1P35222697
FRAT1MAP3K4Q9Y6R4695
FRAT1LRP6O75581525
FRAT1GSK3AP49840477
FRAT1GYS1P13807471
FRAT1EPM2AO95278436
FRAT1WNT1P04628433
FRAT1NHLRC1Q6VVB1430
FRAT1LRP5O75197426
FRAT1MAPK6Q16659425
FRAT1CD244Q9BZW8410

IntAct

28 interactions, top by confidence:

ABTypeScore
AXIN1GSK3Bpsi-mi:“MI:0217”(phosphorylation reaction)0.980
GSK3BAXIN1psi-mi:“MI:0914”(association)0.980
FRAT1GSK3Bpsi-mi:“MI:0407”(direct interaction)0.810
GSK3AAXIN1psi-mi:“MI:0914”(association)0.800
FRAT1GSK3Apsi-mi:“MI:0915”(physical association)0.740
Ctnnb1GSK3Bpsi-mi:“MI:0217”(phosphorylation reaction)0.620
AXIN1GSK3Bpsi-mi:“MI:0914”(association)0.520
AXIN1psi-mi:“MI:0914”(association)0.520
FRAT1psi-mi:“MI:0407”(direct interaction)0.440
FRAT1GSK3Bpsi-mi:“MI:0407”(direct interaction)0.440
EIF2B5GSK3Bpsi-mi:“MI:0217”(phosphorylation reaction)0.440
GSK3BSEC16Apsi-mi:“MI:0914”(association)0.420
GRNFRAT1psi-mi:“MI:0915”(physical association)0.370
KRT18FRAT1psi-mi:“MI:0915”(physical association)0.370
PLSCR1FRAT1psi-mi:“MI:0915”(physical association)0.370
PSMA3FRAT1psi-mi:“MI:0915”(physical association)0.370
FRAT1LTBP4psi-mi:“MI:0915”(physical association)0.370
KCNK5FRAT1psi-mi:“MI:0915”(physical association)0.370
FRAT1LAMC3psi-mi:“MI:0915”(physical association)0.370
FRAT1LMAN2psi-mi:“MI:0915”(physical association)0.370
FRAT1TDRD7psi-mi:“MI:0915”(physical association)0.370
RABEP2FRAT1psi-mi:“MI:0915”(physical association)0.370
GPRASP2FRAT1psi-mi:“MI:0915”(physical association)0.370
FRAT1PIAS1psi-mi:“MI:0914”(association)0.350

BioGRID (24): FRAT1 (Affinity Capture-Western), FRAT1 (Affinity Capture-Luminescence), GSK3A (Affinity Capture-MS), GSK3B (Affinity Capture-MS), KRAS (Affinity Capture-MS), PIAS1 (Affinity Capture-MS), FRAT1 (Affinity Capture-MS), DVL1 (Affinity Capture-Western), FRAT1 (Affinity Capture-MS), FRAT1 (Protein-peptide), GPRASP2 (Two-hybrid), LAMC3 (Two-hybrid), KRT18 (Two-hybrid), GRN (Two-hybrid), PLSCR1 (Two-hybrid)

ESM2 similar proteins: A0A0U1RRK4, A0A1W2PPE3, A0A1W2PR82, A0A2Z4LIS9, A2VE02, A4D1S0, A5PKC7, A5PL33, A6H7B4, A6NEL2, A6QP24, A6QPM6, A8MTW9, A8MYA2, D3ZAQ5, D4AAA5, E7EW31, O75474, O75638, O89113, O94850, P0C7X2, P14652, P50617, P70339, Q2KIS6, Q3UN58, Q5JPB2, Q5VZ46, Q6GQX2, Q6NZ36, Q6ZSJ8, Q6ZW13, Q76NI1, Q7TNS8, Q80TS7, Q86UU5, Q8IWN7, Q8N6K4, Q8N944

Diamond homologs: O75474, O93343, P70339, Q8K025, Q92837

SIGNOR signaling

7 interactions.

AEffectBMechanism
PRKACAdown-regulatesFRAT1phosphorylation
FRAT1up-regulatesGSK3B/Axin/APCbinding
GSK3B“down-regulates activity”FRAT1phosphorylation
PKA“down-regulates activity”FRAT1phosphorylation
FRAT1up-regulatesGSK3Bbinding
DVL3up-regulatesFRAT1binding
FRAT1“up-regulates activity”EIF2B5binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance48
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

120 predictions. Top by Δscore:

VariantEffectΔscore
10:97320132:T:Gdonor_gain0.8800
10:97319481:G:GTdonor_gain0.8100
10:97319475:G:GTdonor_gain0.7900
10:97321024:TAAAG:Tacceptor_gain0.7700
10:97320692:T:Gdonor_gain0.7300
10:97321683:A:AGacceptor_gain0.7100
10:97321684:G:GGacceptor_gain0.7100
10:97319540:GCA:Gdonor_gain0.6700
10:97319493:G:GTdonor_gain0.6500
10:97319508:G:GTdonor_gain0.6500
10:97319514:G:GTdonor_gain0.6400
10:97320137:TGCA:Tdonor_gain0.6400
10:97319542:A:AGdonor_gain0.6300
10:97319543:G:GGdonor_gain0.6300
10:97319438:GCCC:Gdonor_gain0.6000
10:97320096:G:GTdonor_gain0.5900
10:97321025:AAAG:Aacceptor_gain0.5900
10:97319517:G:GTdonor_gain0.5700
10:97320422:G:GTdonor_gain0.5600
10:97320681:G:GTdonor_gain0.5600
10:97320436:C:Tdonor_gain0.5500
10:97321684:GTCA:Gacceptor_gain0.5500
10:97319472:G:GTdonor_gain0.5400
10:97320394:G:GTdonor_gain0.5400
10:97319572:T:TAdonor_gain0.5300
10:97319573:G:GAdonor_gain0.5300
10:97321685:T:Gacceptor_gain0.5300
10:97319613:G:GTdonor_gain0.5200
10:97319545:C:Adonor_gain0.5100
10:97320335:C:Tdonor_gain0.4900

AlphaMissense

1721 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:97320095:G:CK214N0.996
10:97320095:G:TK214N0.996
10:97320082:G:TG210V0.995
10:97320091:T:AI213N0.995
10:97320091:T:CI213T0.995
10:97320091:T:GI213S0.993
10:97320082:G:AG210E0.991
10:97320099:G:CA216P0.991
10:97320088:T:CL212P0.987
10:97320070:T:CL206P0.986
10:97320088:T:AL212H0.984
10:97320094:A:TK214M0.984
10:97320081:G:AG210R0.982
10:97320081:G:CG210R0.982
10:97319593:T:GI47S0.980
10:97320086:C:AN211K0.980
10:97320086:C:GN211K0.980
10:97320100:C:AA216D0.979
10:97319593:T:AI47N0.978
10:97320096:G:AE215K0.972
10:97319581:T:CL43P0.969
10:97320093:A:GK214E0.967
10:97320097:A:TE215V0.967
10:97320110:G:CR219S0.967
10:97320110:G:TR219S0.967
10:97320085:A:TN211I0.966
10:97320079:C:TS209F0.964
10:97320097:A:GE215G0.961
10:97320094:A:CK214T0.960
10:97319593:T:CI47T0.959

dbSNP variants (sampled 300 via entrez): RS1000145657 (10:97321957 T>C), RS1000157063 (10:97321646 A>G), RS1001935435 (10:97320796 C>A), RS1002458847 (10:97317679 C>T), RS1002617535 (10:97317936 T>C), RS1003040469 (10:97322189 T>G), RS1003331162 (10:97321837 T>C), RS1003491854 (10:97319061 C>T), RS1004233060 (10:97319216 G>A,C), RS1004578398 (10:97319055 C>A), RS1005238635 (10:97319091 G>A), RS1006343498 (10:97321464 C>G,T), RS1006374489 (10:97321760 T>G), RS1006496072 (10:97317707 C>A,G), RS1007054172 (10:97321530 G>T)

Disease associations

OMIM: gene MIM:602503 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST90002388_572Lymphocyte count2.000000e-12
GCST90002407_310White blood cell count2.000000e-77
GCST90013405_22Liver enzyme levels (alanine transaminase)3.000000e-12

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004587lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

44 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Cyclosporinedecreases expression3
Estradioldecreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Valproic Aciddecreases expression, increases expression2
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
propionaldehydedecreases expression1
afimoxifenedecreases reaction, decreases expression1
butyraldehydedecreases expression1
ochratoxin Adecreases expression1
ferrous chloridedecreases expression1
S-(1,2-dichlorovinyl)cysteineincreases expression, affects response to substance1
pentanaldecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
PKF115-584increases expression1
jinfukangincreases expression, affects cotreatment1
NSC 689534affects binding, decreases expression1
Sunitinibincreases expression1
Arsenic Trioxidedecreases expression1
Acetaminophendecreases expression1
Aldehydesdecreases expression1
Atrazinedecreases expression1
Hexachlorocyclohexaneincreases expression1
Benzo(a)pyrenedecreases expression1
Carbamazepineaffects expression1
Cisplatinaffects cotreatment, increases expression1
Copperaffects binding, decreases expression1
Environmental Pollutantsaffects expression1
Estrogensdecreases expression, decreases reaction1

Cellosaurus cell lines

2 cell lines: 1 transformed cell line, 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D9F2Ubigene HEK293 FRAT1 KOTransformed cell lineFemale
CVCL_E0DAUbigene HeLa FRAT1 KOCancer cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.