KLF17

gene
On this page

Also known as Zfp393FLJ40160

Summary

KLF17 (KLF transcription factor 17, HGNC:18830) is a protein-coding gene on chromosome 1p34.1, encoding Krueppel-like factor 17 (Q5JT82). Transcription repressor that binds to the promoter of target genes and prevents their expression.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within gamete generation. Predicted to be located in chromatin.

Source: NCBI Gene 128209 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 76 total
  • MANE Select transcript: NM_173484

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18830
Approved symbolKLF17
NameKLF transcription factor 17
Location1p34.1
Locus typegene with protein product
StatusApproved
AliasesZfp393, FLJ40160
Ensembl geneENSG00000171872
Ensembl biotypeprotein_coding
OMIM609602
Entrez128209

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000372299, ENST00000476802

RefSeq mRNA: 1 — MANE Select: NM_173484 NM_173484

CCDS: CCDS508

Canonical transcript exons

ENST00000372299 — 4 exons

ExonStartEnd
ENSE000011455214413051244130756
ENSE000012360044412935344130196
ENSE000014574634413323844135140
ENSE000014574704411882144118988

Expression profiles

Bgee: expression breadth broad, 83 present calls, max score 76.33.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9560 / max 136.8984, expressed in 284 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
25880.6180239
25890.134244
25910.12988
25930.03056
25950.02895
25920.00816
25940.00655

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453376.33gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047375.83gold quality
right testisUBERON:000453475.49gold quality
testisUBERON:000047373.89gold quality
smooth muscle tissueUBERON:000113560.69gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099160.25gold quality
spermCL:000001957.32silver quality
stromal cell of endometriumCL:000225557.29gold quality
lower esophagus muscularis layerUBERON:003583356.56gold quality
lower esophagusUBERON:001347356.52gold quality
upper leg skinUBERON:000426254.88silver quality
right lungUBERON:000216754.36gold quality
left adrenal glandUBERON:000123453.92gold quality
right adrenal glandUBERON:000123353.59gold quality
adult organismUBERON:000702353.58gold quality
left adrenal gland cortexUBERON:003582553.21gold quality
urinary bladderUBERON:000125552.56gold quality
right adrenal gland cortexUBERON:003582752.36gold quality
adrenal glandUBERON:000236952.22gold quality
adrenal cortexUBERON:000123552.13gold quality
lower esophagus mucosaUBERON:003583451.87gold quality
body of uterusUBERON:000985350.64gold quality
myometriumUBERON:000129650.37gold quality
esophagogastric junction muscularis propriaUBERON:003584150.00gold quality
gall bladderUBERON:000211049.16gold quality
vermiform appendixUBERON:000115449.08gold quality
left uterine tubeUBERON:000130348.61gold quality
upper lobe of left lungUBERON:000895248.41gold quality
upper lobe of lungUBERON:000894848.22gold quality
muscle layer of sigmoid colonUBERON:003580547.70gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.11
E-MTAB-8060no65.11

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

5 targets.

TargetRegulation
CCND1Repression
CD44Repression
PARK7
SERPINE1Repression
TWIST1Repression

JASPAR motifs

MotifNameFamily
MA1514.1KLF17Three-zinc finger Kruppel-related
MA1514.2KLF17Three-zinc finger Kruppel-related

JASPAR matrix evidence (PMIDs): PMID:11443140

Upstream regulators (CollecTRI, top): TP53, TWIST1

miRNA regulators (miRDB)

42 targeting KLF17, 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-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-477599.9875.006394
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-590-3P99.9674.346478
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-129-5P99.8870.263273
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-205299.7969.372031
HSA-MIR-370-5P99.7866.81706
HSA-MIR-320299.6667.702737
HSA-MIR-448999.5065.56785
HSA-MIR-504-3P99.3067.181745
HSA-MIR-877-3P99.0968.101637
HSA-MIR-129498.9169.261030
HSA-MIR-998698.9169.281024
HSA-MIR-3194-3P98.8366.221167
HSA-MIR-4755-3P98.7765.591915
HSA-MIR-2467-3P98.6567.181969
HSA-MIR-210-5P98.5764.37832
HSA-MIR-4726-3P98.4963.891385

Literature-anchored findings (GeneRIF, showing 26)

  • KLF17 is a new member of the Sp/KLF family of transcription factors. (PMID:16460907)
  • demonstrate that KLF17 expression is significantly downregulated in primary human breast cancer samples and that the combined expression pattern of KLF17 and Id1 can serve as a potential biomarker for lymph node metastasis in breast cancer (PMID:19801974)
  • KLF17 has a role in transcriptional regulation of metastasis by Id1 [review] (PMID:19951400)
  • it is possible that KLF17 inhibits tumor growth in lung adenocarcinoma. (PMID:22240024)
  • Overall, these findings suggest a repressing role of KLF17 in tumor invasion (PMID:23325444)
  • KLF17 may have an oncogenic role during EEC progression via initiating EMT through the regulation of TWIST1 (PMID:24220291)
  • KLF17 might be one of the downstream signalling molecules of DJ-1. (PMID:24504364)
  • The reduced expression of KLF17 protein in gastric cancer was correlated with tumor size, pN stage and lymphovascular invasion and was an independent predictor for poor survival in patients undergoing surgery for gastric cancer. (PMID:24947617)
  • The reduced expression of KLF17 promoted the motility and proliferation ability of TPC1 cells by altering the expression of tight junction protein 1 and Snai1, and activating the AKT pathway by upregulating inhibitor of DNA binding 1. (PMID:25109837)
  • mutant p53 enhances cancer progression by inhibiting KLF17 expression in invasive breast carcinoma cells (PMID:25111898)
  • In this review, we focus on the functions, roles, and regulatory networks of these five KLFs in HCC, summarize key pathways, and propose areas for further investigation (PMID:25652467)
  • A small subset of Myoepithelial tumors harbor FUS rearrangements, two thirds of them being associated with KLF17 fusion. (PMID:25706482)
  • KLF17 empowers TGF-beta/Smad signaling by targeting Smad3-dependent pathway to suppress tumor growth and metastasis during cancer progression. (PMID:25766320)
  • Tumor-suppressive p53 signaling is critical for KLF17 to inhibit cancer metastasis in Non-small Cell Lung Cancer. (PMID:25911104)
  • Suggest that KLF17 inhibits esophageal carcinoma development and may serve as a potential therapeutic target. (PMID:26617836)
  • Enhanced KLF17 expression sensitizes ERalpha-positive breast cancer cells to endocrine therapy.KLF17-ERalpha interaction plays a potential role in inhibition of ERalpha-dependent breast cancer progression. (PMID:27107895)
  • Low Expressions of KLF17 is associated with lung adenocarcinoma. (PMID:28454121)
  • The above data show that normal levels of melatonin may help in preventing breast cancer metastasis through inhibiting DJ-1/KLF17/ID-1 signaling pathway. The combination of melatonin and taxol is a potent candidate against breast cancer metastasis, better than using melatonin or taxol as a single drug (PMID:30260001)
  • Results revealed that KLF17 expression was abnormally decreased in colorectal cancer (CRC) and associated with lymph node metastasis and unfavorable overall survival. Moreover, ectopic KLF17 expression suppressed CRC cell growth and invasion in vitro and in vivo. In addition, the downregulation of KLF17 was associated with the hypermethylation of the CpG nucleotides on the KLF17 promoter. (PMID:31545467)
  • Overexpression of KLF17 Predicts a Favorable Prognosis in Patients with Oral Squamous Cell Carcinoma: A Retrospective Study. (PMID:32019121)
  • Kruppel-like factor 17 upregulates uterine corin expression and promotes spiral artery remodeling in pregnancy. (PMID:32719113)
  • Precision hyperthermia-induced miRNA-409-3p upregulation inhibits migration, invasion, and EMT of gastric cancer cells by targeting KLF17. (PMID:33667708)
  • Up-regulation of KLF17 expression increases the sensitivity of gastric cancer to 5-fluorouracil. (PMID:33960231)
  • KLF17 promotes human naive pluripotency but is not required for its establishment. (PMID:34661235)
  • Effect of KLF17 overexpression on epithelial-mesenchymal transition of gastric cancer cells. (PMID:34738482)
  • KLF17 promotes human naive pluripotency through repressing MAPK3 and ZIC2. (PMID:35391627)

Cross-species orthologs

16 orthologs

OrganismSymbolGene ID
danio_rerioklf1ENSDARG00000017400
danio_rerioklf5lENSDARG00000018757
danio_rerioklf17ENSDARG00000038792
danio_rerioklf2bENSDARG00000040432
danio_rerioklf2aENSDARG00000042667
danio_rerioklf13ENSDARG00000061368
danio_reriozgc:153115ENSDARG00000069342
danio_reriosi:ch211-117k10.3ENSDARG00000090914
danio_reriosp5lENSDARG00000115868
mus_musculusKlf17ENSMUSG00000048626
rattus_norvegicusKlf17ENSRNOG00000019479
drosophila_melanogasterKlf15FBGN0025679
drosophila_melanogasterlunaFBGN0040765
drosophila_melanogasterCG42741FBGN0261705
drosophila_melanogasterdar1FBGN0263239
caenorhabditis_elegansWBGENE00018990

Paralogs (22): KLF6 (ENSG00000067082), KLF8 (ENSG00000102349), KLF5 (ENSG00000102554), KLF1 (ENSG00000105610), KLF3 (ENSG00000109787), KLF7 (ENSG00000118263), KLF12 (ENSG00000118922), KLF9 (ENSG00000119138), KLF2 (ENSG00000127528), KLF16 (ENSG00000129911), KLF4 (ENSG00000136826), KLF10 (ENSG00000155090), KLF15 (ENSG00000163884), SP8 (ENSG00000164651), KLF13 (ENSG00000169926), SP7 (ENSG00000170374), KLF11 (ENSG00000172059), SP6 (ENSG00000189120), SP5 (ENSG00000204335), SP9 (ENSG00000217236), KLF14 (ENSG00000266265), KLF18 (ENSG00000283039)

Protein

Protein identifiers

Krueppel-like factor 17Q5JT82 (reviewed: Q5JT82)

Alternative names: Zinc finger protein 393

All UniProt accessions (2): Q5JT82, A0A0U1RR65

UniProt curated annotations — full annotation on UniProt →

Function. Transcription repressor that binds to the promoter of target genes and prevents their expression. Acts as a negative regulator of epithelial-mesenchymal transition and metastasis in breast cancer. Specifically binds the 5’-CACCC-3’ sequence in the promoter of ID1, a key metastasis regulator in breast cancer, and repress its expression. May be a germ cell-specific transcription factor that plays important roles in spermatid differentiation and oocyte development.

Subcellular location. Nucleus.

Similarity. Belongs to the Sp1 C2H2-type zinc-finger protein family.

RefSeq proteins (1): NP_775755* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096

UniProt features (14 total): sequence variant 4, zinc finger region 3, region of interest 3, compositionally biased region 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5JT82-F154.300.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, chr1p34, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, FOSTER_KDM1A_TARGETS_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE13522_WT_VS_IFNG_KO_SKIN_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR4795_3P, GOLDRATH_EFF_VS_MEMORY_CD8_TCELL_DN, MIR9983_3P, MIR129_5P, MIR2052, MIR7156_3P, MIR6872_3P

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (9): transcription cis-regulatory region binding (GO:0000976), 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 factor activity (GO:0003700), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
transcription by RNA polymerase II1
transcription regulatory region nucleic acid binding1
sequence-specific double-stranded DNA binding1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transcription cis-regulatory region binding1
transcription regulator activity1
transition metal ion binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
cation binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

764 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KLF17ID1P41134771
KLF17ID2Q02363702
KLF17ARFGAP2Q8N6H7666
KLF17TFCP2L1Q9NZI6652
KLF17ARGFXA6NJG6591
KLF17DPPA5A6NC42588
KLF17WNT2P09544555
KLF17DPPA3Q6W0C5521
KLF17SLC5A5Q92911495
KLF17SUSD2Q9UGT4480
KLF17TP53P04637477
KLF17POU5F1P31359467
KLF17FUSP35637464
KLF17FGF4P08620457
KLF17A0A0J9YW77A0A0J9YW77457

IntAct

17 interactions, top by confidence:

ABTypeScore
KLF17CIB3psi-mi:“MI:0915”(physical association)0.720
CIB3KLF17psi-mi:“MI:0915”(physical association)0.720
KLF17COL6A1psi-mi:“MI:0915”(physical association)0.400
CCL24KLF17psi-mi:“MI:0915”(physical association)0.370
CCL26KLF17psi-mi:“MI:0915”(physical association)0.370
CCL27KLF17psi-mi:“MI:0915”(physical association)0.370
KLF17psi-mi:“MI:0915”(physical association)0.370
IL1RNKLF17psi-mi:“MI:0915”(physical association)0.370
IL23AKLF17psi-mi:“MI:0915”(physical association)0.370
IL31KLF17psi-mi:“MI:0915”(physical association)0.370
TNFSF10KLF17psi-mi:“MI:0915”(physical association)0.370
CIB3KLF17psi-mi:“MI:0915”(physical association)0.000

BioGRID (3): KLF17 (Two-hybrid), KLF17 (Two-hybrid), KLF17 (Proximity Label-MS)

ESM2 similar proteins: A0A0A7EPL0, A2RV66, A4QP16, A6QPF4, C4QM85, F4JYG0, O35892, P11836, P13386, P19437, P20490, P41739, P53762, P56645, P70326, P79778, Q01362, Q148B6, Q29131, Q3C1V0, Q3C2E2, Q3SA47, Q3UNB8, Q3V3Q4, Q3YBM2, Q5I2P1, Q5JT82, Q5R8D6, Q5R8E0, Q60HE7, Q68FU0, Q6A058, Q8BVM2, Q8N1N2, Q8NDZ0, Q8QGQ8, Q8WUU8, Q920C4, Q92540, Q96HJ5

Diamond homologs: A0A0U1RQI7, C7EMF5, Q00453, Q5JT82, Q8CFA7, B5DE03, B7ZSG3, O08876, O14901, O62651, O89091, P19544, P22561, P49952, P49953, P50902, P57682, P79958, Q13118, Q13887, Q19A41, Q60980, Q8K1S5, O35738, O35819, Q60843, Q9ET58, Q9TZ64, Q9VZN4, Q9Y4X4, Q8TD94, Q14V87, Q19A40, Q65ZG6, Q13351, O08584, O15090, O35739, O43474, O62259

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign10
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

471 predictions. Top by Δscore:

VariantEffectΔscore
1:44118989:G:GGdonor_gain1.0000
1:44118989:GT:Gdonor_loss1.0000
1:44130730:G:GTdonor_gain0.9900
1:44130731:A:Tdonor_gain0.9900
1:44130506:TCCCA:Tacceptor_loss0.9800
1:44130507:CCCAG:Cacceptor_loss0.9800
1:44130508:CCAG:Cacceptor_loss0.9800
1:44130509:CAGG:Cacceptor_loss0.9800
1:44130510:AGGTG:Aacceptor_loss0.9800
1:44130511:G:GAacceptor_loss0.9800
1:44130567:T:TAacceptor_gain0.9800
1:44130500:T:TAacceptor_loss0.9700
1:44130749:GTCCT:Gdonor_gain0.9700
1:44130750:TCCTT:Tdonor_gain0.9700
1:44118986:CAG:Cdonor_gain0.9600
1:44118987:AG:Adonor_gain0.9600
1:44118988:GG:Gdonor_gain0.9600
1:44129432:GCC:Gdonor_gain0.9600
1:44130567:TGATG:Tacceptor_gain0.9600
1:44130723:A:Tdonor_gain0.9600
1:44118989:G:GAdonor_gain0.9500
1:44118990:T:Adonor_gain0.9500
1:44130753:TTAG:Tdonor_loss0.9500
1:44130754:TAGG:Tdonor_loss0.9500
1:44130755:AG:Adonor_loss0.9500
1:44130756:GGTC:Gdonor_loss0.9500
1:44130757:GT:Gdonor_loss0.9500
1:44130758:T:Gdonor_loss0.9500
1:44118985:CCAGG:Cdonor_gain0.9400
1:44118986:CAGG:Cdonor_gain0.9400

AlphaMissense

2548 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:44130556:T:CF324L1.000
1:44130558:C:AF324L1.000
1:44130558:C:GF324L1.000
1:44130619:T:CC345R1.000
1:44130640:T:CF352L1.000
1:44130641:T:CF352S1.000
1:44130642:C:AF352L1.000
1:44130642:C:GF352L1.000
1:44130139:T:AC290S0.999
1:44130140:G:CC290S0.999
1:44130151:T:GY294D0.999
1:44130170:T:CL300P0.999
1:44130178:C:GH303D0.999
1:44130180:C:AH303Q0.999
1:44130180:C:GH303Q0.999
1:44130182:A:CQ304P0.999
1:44130185:G:CR305P0.999
1:44130192:C:AH307Q0.999
1:44130192:C:GH307Q0.999
1:44130531:C:GC315W0.999
1:44130545:G:AC320Y0.999
1:44130546:T:GC320W0.999
1:44130563:G:CR326P0.999
1:44130583:C:GH333D0.999
1:44130585:T:AH333Q0.999
1:44130585:T:GH333Q0.999
1:44130597:C:AH337Q0.999
1:44130597:C:GH337Q0.999
1:44130619:T:AC345S0.999
1:44130620:G:CC345S0.999

dbSNP variants (sampled 300 via entrez): RS1000004265 (1:44132209 G>T), RS1000011096 (1:44135182 C>A), RS1000048994 (1:44055072 C>A), RS1000051772 (1:44047096 T>G), RS1000083723 (1:44051260 T>G), RS1000126732 (1:44093639 C>A,T), RS1000236288 (1:44099073 T>A,C), RS1000242487 (1:44109204 A>G), RS1000300871 (1:44081223 A>T), RS1000413804 (1:44093345 G>A), RS1000442500 (1:44071169 C>T), RS1000472778 (1:44044465 C>A), RS1000503725 (1:44085326 G>A), RS1000556425 (1:44126842 T>C), RS1000625215 (1:44079500 A>G)

Disease associations

OMIM: gene MIM:609602 | 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
GCST004025_7Systemic juvenile idiopathic arthritis1.000000e-06
GCST005722_1Milk allergy (maternal genetic effects)2.000000e-06
GCST010002_357Refractive error3.000000e-13

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005939parental genotype effect measurement
EFO:0007019milk allergy measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
napabucasindecreases expression1
bisphenol Aaffects cotreatment, decreases methylation1
terbufosincreases methylation1
(+)-JQ1 compounddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantdecreases methylation, affects cotreatment1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Diethylhexyl Phthalateincreases expression1
Fonofosincreases methylation1
Fenfluramineincreases expression1
Parathionincreases methylation1
Plant Extractsaffects cotreatment, decreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_HC80HEK293 eGFP-KLF17Transformed cell lineFemale

Clinical trials (associated diseases)

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