KLF3

Summary

KLF3 (KLF transcription factor 3, HGNC:16516) is a protein-coding gene on chromosome 4p14, encoding Krueppel-like factor 3 (P57682). Binds to the CACCC box of erythroid cell-expressed genes.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm.

Source: NCBI Gene 51274 — RefSeq curated summary.

At a glance

• GWAS associations: 35
• Clinical variants (ClinVar): 49 total
• Transcription factor: yes — 17 downstream targets (CollecTRI)
• MANE Select transcript: NM_016531

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16516
Approved symbol	KLF3
Name	KLF transcription factor 3
Location	4p14
Locus type	gene with protein product
Status	Approved
Aliases	BKLF
Ensembl gene	ENSG00000109787
Ensembl biotype	protein_coding
OMIM	609392
Entrez	51274

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

ENST00000261438, ENST00000482150, ENST00000514033, ENST00000862197, ENST00000928716, ENST00000958520, ENST00000958521, ENST00000958522

RefSeq mRNA: 1 — MANE Select: NM_016531 NM_016531

CCDS: CCDS3444

Canonical transcript exons

ENST00000261438 — 6 exons

Exon	Start	End
ENSE00000710406	38694746	38694906
ENSE00000710409	38689729	38689879
ENSE00000710413	38688585	38689071
ENSE00001014985	38680587	38680682
ENSE00001389935	38664199	38664461
ENSE00001417431	38697082	38701517

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 97.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.9549 / max 1018.2123, expressed in 1808 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
47334	20.7163	1770
47333	14.6103	1768
47337	4.0340	1407
47336	2.6665	1321
47330	1.3881	713
47329	1.1180	649
47335	0.9065	604
47332	0.8848	500
47331	0.4366	209
47338	0.1937	97

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper leg skin	UBERON:0004262	97.65	gold quality
penis	UBERON:0000989	97.44	gold quality
esophagus squamous epithelium	UBERON:0006920	97.35	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.28	gold quality
jejunal mucosa	UBERON:0000399	97.09	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.04	gold quality
trabecular bone tissue	UBERON:0002483	96.97	gold quality
colonic mucosa	UBERON:0000317	96.78	gold quality
pharyngeal mucosa	UBERON:0000355	96.77	gold quality
oral cavity	UBERON:0000167	96.50	gold quality
gingiva	UBERON:0001828	96.31	gold quality
mammalian vulva	UBERON:0000997	96.26	gold quality
gingival epithelium	UBERON:0001949	96.19	gold quality
skin of hip	UBERON:0001554	96.08	gold quality
epithelium of esophagus	UBERON:0001976	95.74	gold quality
parietal pleura	UBERON:0002400	95.58	gold quality
germinal epithelium of ovary	UBERON:0001304	95.32	gold quality
rectum	UBERON:0001052	95.26	gold quality
adrenal tissue	UBERON:0018303	95.12	gold quality
urethra	UBERON:0000057	94.95	gold quality
amniotic fluid	UBERON:0000173	94.81	gold quality
skin of abdomen	UBERON:0001416	94.73	gold quality
palpebral conjunctiva	UBERON:0001812	94.71	gold quality
synovial joint	UBERON:0002217	94.71	gold quality
skin of leg	UBERON:0001511	94.19	gold quality
bone marrow	UBERON:0002371	94.08	gold quality
zone of skin	UBERON:0000014	94.06	gold quality
monocyte	CL:0000576	93.89	gold quality
superficial temporal artery	UBERON:0001614	93.72	gold quality
gall bladder	UBERON:0002110	93.64	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-10042	yes	23.80
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

17 targets.

Target	Regulation
ADAM2
BIK
C1QTNF12	Activation
C4A
CALCA
CEBPA	Unknown
CKM
EIF3K
HBA1
HBE1	Unknown
HBG1	Unknown
HP
ITGB7
KLF3
KLF8	Repression
LTB
WEE1

JASPAR motifs

Motif	Name	Family
MA1516.1	KLF3	Three-zinc finger Kruppel-related
MA1516.2	KLF3	Three-zinc finger Kruppel-related

JASPAR matrix evidence (PMIDs): PMID:11443140

Upstream regulators (CollecTRI, top): IL17A, KLF1, KLF3

miRNA regulators (miRDB)

327 targeting KLF3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-5688	99.96	73.23	4504

Literature-anchored findings (GeneRIF, showing 23)

• The recruitment of CtBP and sumoylation are required for full repression by BKLF. (PMID:15684403)
• KLF3 is an important regulator of several biological processes, including adipogenesis, erythropoiesis, and B cell development. (Review) (PMID:21360637)
• Low KLF3 is associated with acute myeloid leukemia. (PMID:21470678)
• B cell differentiation is significantly impaired in the bone marrow, spleen, and peritoneal cavity of Klf3 null mice; the defects are cell autonomous. (PMID:22003205)
• A feedback loop consisting of microRNA 23a/27a and the beta-like globin suppressors KLF3 and SP1 regulates globin gene expression. (PMID:23918807)
• Among the mechanosensitive genes, the two transcription factors, HoxA5 and Klf3, contain cAMP-response-elements methylation of which could serve as a mechanosensitive master switch in gene expression in atherosclerosis. (Review) (PMID:25979369)
• Klf-3 expression is downregulated in human metastatic sarcomas, and Klf-3 levels negatively correlate with miR-182 expression. (PMID:26314219)
• Low KLF3 expression is associated with colorectal cancer. (PMID:28423541)
• These data demonstrate that miR-326/Sp1/KLF3 regulatory axis is involved in the development of lung cancer. miR-326 could bind to 3’UTR of Sp1 but not KLF3 and decreased the accumulation of Sp1, which further indirectly reduced KLF3 expression and inactivated JAK2/STAT3 and PI3K/AKT signaling pathways in vitro and in vivo. (PMID:30485570)
• bioinformatics analysis and in vitro experiments indicated that the role of KLF3 in lung cancer metastasis is dependent on the STAT3 signaling pathway. Overall, our data indicated the crucial function of KLF3 in lung cancer metastasis and suggested opportunities to improve the therapy of patients with lung cancer. (PMID:31486564)
• LncRNA NEAT1/miR-1224/KLF3 contributes to cell proliferation, apoptosis and invasion in lung cancer. (PMID:31646570)
• Expression of human Kruppel-like factor 3 in peripheral blood as a promising biomarker for acute leukemia. (PMID:32101374)
• Unravelling Structure, Localization, and Genetic Crosstalk of KLF3 in Human Breast Cancer. (PMID:33490232)
• microRNA-21-5p from M2 macrophage-derived extracellular vesicles promotes the differentiation and activity of pancreatic cancer stem cells by mediating KLF3. (PMID:33728488)
• Hepatic Meteorin-like and Kruppel-like Factor 3 are Associated with Weight Loss and Liver Injury. (PMID:34407548)
• Exosome miR-23a-3p from Osteoblast Alleviates Spinal Cord Ischemia/Reperfusion Injury by Down-Regulating KLF3-Activated CCNL2 Transcription. (PMID:34937039)
• Fat mass and obesity associated (FTO)-mediated N6-methyladenosine modification of Kruppel-like factor 3 (KLF3) promotes osteosarcoma progression. (PMID:35311620)
• Bone mesenchymal stem cells (BMSCs)-derived exosomal microRNA-21-5p regulates Kruppel-like factor 3 (KLF3) to promote osteoblast proliferation in vitro. (PMID:35549815)
• KLF3 Transcription Activates WNT1 and Promotes the Growth and Metastasis of Gastric Cancer via Activation of the WNT/beta-Catenin Signaling Pathway. (PMID:36827869)
• microRNA-92b-3p augments colon cancer development through inhibiting KLF3. (PMID:37597242)
• Pan-cancer analysis of Kruppel-like factor 3 and its carcinogenesis in pancreatic cancer. (PMID:37600783)
• Decreased KLF3 Expression via miR-660-5p Targeting Suppresses Gastric Cancer Cell Progression. (PMID:37945021)
• Molecular Expression and Prognostic Implications of Kruppel-Like Factor 3 (KLF3) in Clear Cell Renal Cell Carcinoma. (PMID:38073441)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	klf3	ENSDARG00000015495
mus_musculus	Klf3	ENSMUSG00000029178
rattus_norvegicus	Klf3	ENSRNOG00000002163
drosophila_melanogaster	luna	FBGN0040765

Paralogs (22): KLF6 (ENSG00000067082), KLF8 (ENSG00000102349), KLF5 (ENSG00000102554), KLF1 (ENSG00000105610), KLF7 (ENSG00000118263), KLF12 (ENSG00000118922), KLF9 (ENSG00000119138), KLF2 (ENSG00000127528), KLF16 (ENSG00000129911), KLF4 (ENSG00000136826), KLF10 (ENSG00000155090), KLF15 (ENSG00000163884), SP8 (ENSG00000164651), KLF13 (ENSG00000169926), SP7 (ENSG00000170374), KLF17 (ENSG00000171872), KLF11 (ENSG00000172059), SP6 (ENSG00000189120), SP5 (ENSG00000204335), SP9 (ENSG00000217236), KLF14 (ENSG00000266265), KLF18 (ENSG00000283039)

Protein

Protein identifiers

Krueppel-like factor 3 — P57682 (reviewed: P57682)

Alternative names: Basic krueppel-like factor, CACCC-box-binding protein BKLF, TEF-2

All UniProt accessions (1): P57682

UniProt curated annotations — full annotation on UniProt →

Function. Binds to the CACCC box of erythroid cell-expressed genes. May play a role in hematopoiesis.

Subunit / interactions. Monomer.

Subcellular location. Nucleus.

Post-translational modifications. Sumoylated with SUMO1. Sumoylation is enhanced by PIAS1, PIAS2alpha and PIAS2beta, and PIAS4, but not by Pc2. Enhances transcriptional repression, but has no effect on DNA binding. Sumoylation on Lys-198 is the major site.

Domain organisation. The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors. In KLF3, the motif is inactive.

Miscellaneous. May be due to intron retention.

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

Isoforms (2)

UniProt ID	Names	Canonical?
P57682-1	1	yes
P57682-2	2

RefSeq proteins (1): NP_057615* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (27 total): modified residue 8, cross-link 4, zinc finger region 3, sequence conflict 3, region of interest 2, short sequence motif 2, compositionally biased region 2, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P57682-F1	54.04	0.13

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 (12): 71, 92, 101, 108, 111, 216, 224, 250, 10, 68, 196, 198

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 351 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, FREAC2_01, HNF3ALPHA_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GGGTGGRR_PAX4_03, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, CHANDRAN_METASTASIS_DN, EFC_Q6, MARTINEZ_RB1_TARGETS_UP, SOX9_B1, GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS, HFH8_01, FOXJ2_01, HFH4_01

GO Biological Process (4): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), hemopoiesis (GO:0030097), cellular response to endothelin (GO:1990859)

GO Molecular Function (9): 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), RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): chromatin (GO:0000785), nucleoplasm (GO:0005654), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
regulation of DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription cis-regulatory region binding	2
cellular anatomical structure	2
negative regulation of DNA-templated transcription	1
cell development	1
cellular response to peptide hormone stimulus	1
response to endothelin	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
transcription regulator activity	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
chromosome	1
nuclear lumen	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1228 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KLF3	CTBP1	Q13363	988
KLF3	CTBP2	P56545	972
KLF3	ZNF217	O75362	669
KLF3	ZNF516	Q92618	648
KLF3	ZFPM1	Q8IX07	644
KLF3	HDAC2	Q92769	642
KLF3	RCOR1	Q9UKL0	634
KLF3	GATA1	P15976	587
KLF3	CBX2	Q14781	586
KLF3	SIN3A	Q96ST3	585
KLF3	SOX6	P35712	541
KLF3	SRF	P11831	500
KLF3	SPI1	P17947	487
KLF3	HDAC1	Q13547	476
KLF3	UBE2I	P50550	470

IntAct

169 interactions, top by confidence:

A	B	Type	Score
FHL3	KLF3	psi-mi:“MI:0915”(physical association)	0.810
KLF3	FHL3	psi-mi:“MI:0915”(physical association)	0.810
KLF3	TRAF2	psi-mi:“MI:0915”(physical association)	0.720
TRAF2	KLF3	psi-mi:“MI:0915”(physical association)	0.720
KLF3	EHMT2	psi-mi:“MI:0915”(physical association)	0.660
KLF3	GRN	psi-mi:“MI:0915”(physical association)	0.660
ATXN1	KLF3	psi-mi:“MI:0915”(physical association)	0.660
KLF3	CTBP1	psi-mi:“MI:0915”(physical association)	0.620
CTBP1	KLF3	psi-mi:“MI:0915”(physical association)	0.620
KLF3	EHMT2	psi-mi:“MI:0915”(physical association)	0.560
KLF3	LHX8	psi-mi:“MI:0915”(physical association)	0.560
KLF3	DVL3	psi-mi:“MI:0915”(physical association)	0.560
EHMT2	KLF3	psi-mi:“MI:0915”(physical association)	0.560
LHX8	KLF3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (287): KLF3 (Two-hybrid), KLF3 (Two-hybrid), KLF3 (Two-hybrid), KLF3 (Two-hybrid), LHX8 (Two-hybrid), KLF3 (Affinity Capture-RNA), FHL3 (Two-hybrid), UBE2I (Two-hybrid), LSM3 (Two-hybrid), PIAS1 (Two-hybrid), KLF3 (Two-hybrid), CTBP1 (Two-hybrid), KLF3 (Two-hybrid), TRAF2 (Two-hybrid), OTX2 (Two-hybrid)

ESM2 similar proteins: A0A486WWJ9, A0JPB4, A1L1J6, A2VDW9, A4IFJ6, B7ZRM8, B7ZRU9, O08900, O13089, O17862, O42410, O60315, O73590, O75626, P14404, P25932, P34536, P55879, P57682, P81183, Q03112, Q03267, Q13422, Q19418, Q5DU09, Q5R9W9, Q5ZLR2, Q5ZM39, Q60636, Q60980, Q6DBW0, Q6GNP2, Q6INV8, Q6NRM0, Q6XDT4, Q6ZN30, Q86UP3, Q8BMQ3, Q8BU00, Q8I7Z8

Diamond homologs: B5DE03, B7ZSG3, O08876, O14901, O62651, O89091, P19544, P22561, P49952, P49953, P50902, P57682, P79958, Q13118, Q13887, Q19A41, Q5JT82, Q60980, Q8K1S5, O08584, O35738, O35819, O43474, O62259, O70494, O75840, O89090, O95600, P08047, P0CG40, P46099, P58334, Q01714, Q02446, Q02447, Q0VA40, Q13351, Q14V87, Q19A40, Q22678

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
KLF3	“down-regulates quantity by repression”	CEBPA	“transcriptional regulation”
IL17A	“up-regulates quantity by expression”	KLF3	“transcriptional regulation”
IL17A	up-regulates	KLF3	“transcriptional regulation”
KLF3	down-regulates	CEBPA	“transcriptional regulation”
KLF3	“down-regulates quantity by repression”	KLF8	“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Interleukin-10 signaling	5	25.3×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
cell surface receptor signaling pathway via JAK-STAT	5	26.4×	2e-04
positive regulation of type II interferon production	6	24.5×	8e-05
positive regulation of inflammatory response	6	15.8×	3e-04
response to hypoxia	5	8.7×	8e-03
immune response	10	8.6×	8e-05
cell-cell signaling	6	7.6×	5e-03
inflammatory response	8	5.5×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1286 predictions. Top by Δscore:

Variant	Effect	Δscore
4:38664457:GCAAA:G	donor_gain	1.0000
4:38664458:CAAAG:C	donor_loss	1.0000
4:38664459:AAAG:A	donor_loss	1.0000
4:38664460:AA:A	donor_gain	1.0000
4:38664460:AAG:A	donor_loss	1.0000
4:38664461:AGT:A	donor_loss	1.0000
4:38664462:G:GG	donor_gain	1.0000
4:38664462:GTA:G	donor_loss	1.0000
4:38680581:TTCTA:T	acceptor_loss	1.0000
4:38680582:TCTA:T	acceptor_loss	1.0000
4:38680584:TAG:T	acceptor_loss	1.0000
4:38680585:A:AG	acceptor_gain	1.0000
4:38680585:AGG:A	acceptor_loss	1.0000
4:38680586:G:GG	acceptor_gain	1.0000
4:38680586:G:GT	acceptor_loss	1.0000
4:38680680:GTG:G	donor_gain	1.0000
4:38680681:TGGTA:T	donor_loss	1.0000
4:38680682:GGTAA:G	donor_loss	1.0000
4:38680683:G:GG	donor_gain	1.0000
4:38680683:GTAAG:G	donor_loss	1.0000
4:38680684:T:G	donor_loss	1.0000
4:38688581:ATAGT:A	acceptor_loss	1.0000
4:38688582:TAGTC:T	acceptor_loss	1.0000
4:38688583:A:AC	acceptor_loss	1.0000
4:38688583:A:AG	acceptor_gain	1.0000
4:38688584:G:GG	acceptor_gain	1.0000
4:38688584:GTC:G	acceptor_gain	1.0000
4:38688584:GTCA:G	acceptor_gain	1.0000
4:38688584:GTCAT:G	acceptor_gain	1.0000
4:38688773:G:GT	donor_gain	1.0000

AlphaMissense

2252 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:38694834:T:A	C262S	1.000
4:38694834:T:C	C262R	1.000
4:38694835:G:C	C262S	1.000
4:38694849:T:A	C267S	1.000
4:38694849:T:C	C267R	1.000
4:38694850:G:C	C267S	1.000
4:38694861:T:G	Y271D	1.000
4:38694888:C:G	H280D	1.000
4:38694890:C:A	H280Q	1.000
4:38694890:C:G	H280Q	1.000
4:38694900:C:G	H284D	1.000
4:38694902:C:A	H284Q	1.000
4:38694902:C:G	H284Q	1.000
4:38697099:T:A	C292S	1.000
4:38697099:T:C	C292R	1.000
4:38697100:G:C	C292S	1.000
4:38697101:T:G	C292W	1.000
4:38697114:T:A	C297S	1.000
4:38697114:T:C	C297R	1.000
4:38697115:G:A	C297Y	1.000
4:38697115:G:C	C297S	1.000
4:38697116:C:G	C297W	1.000
4:38697126:T:C	F301L	1.000
4:38697127:T:C	F301S	1.000
4:38697128:T:A	F301L	1.000
4:38697128:T:G	F301L	1.000
4:38697133:G:C	R303P	1.000
4:38697145:T:C	L307P	1.000
4:38697153:C:G	H310D	1.000
4:38697155:T:A	H310Q	1.000

dbSNP variants (sampled 300 via entrez): RS1000037535 (4:38693456 A>G), RS1000074352 (4:38696820 T>A), RS1000095 (4:38691230 G>A), RS1000096 (4:38691214 C>A,G,T), RS1000097 (4:38690938 C>A,G), RS1000105949 (4:38680750 A>C,T), RS1000198317 (4:38691279 C>G), RS1000336579 (4:38696203 A>AC,AG), RS1000421192 (4:38689244 G>C), RS1000471652 (4:38684515 G>A,T), RS1000500038 (4:38671346 C>T), RS1000604162 (4:38664925 C>A,G,T), RS1000684947 (4:38677776 G>C), RS1000762593 (4:38686616 G>A), RS1000781228 (4:38673525 A>G)

Disease associations

OMIM: gene MIM:609392 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

35 associations (top):

Study	Trait	p-value
GCST002014_1	Helicobacter pylori serologic status	1.000000e-18
GCST002094_3	Crohn’s disease	4.000000e-14
GCST004600_149	Eosinophil percentage of white cells	7.000000e-17
GCST004606_116	Eosinophil count	2.000000e-48
GCST004610_65	White blood cell count	2.000000e-13
GCST004617_93	Eosinophil percentage of granulocytes	4.000000e-45
GCST004623_34	Neutrophil percentage of granulocytes	4.000000e-14
GCST004624_50	Sum eosinophil basophil counts	4.000000e-43
GCST004627_56	Lymphocyte count	2.000000e-44
GCST004627_57	Lymphocyte count	5.000000e-32
GCST005830_84	Hand grip strength	9.000000e-09
GCST005906_2	Endometriosis or endometrial cancer (pleiotropy)	2.000000e-06
GCST007563_18	Allergic disease (asthma, hay fever or eczema)	2.000000e-10
GCST009597_150	Multiple sclerosis	5.000000e-06
GCST009798_22	Asthma	4.000000e-17
GCST010699_6	Brain morphology (min-P)	8.000000e-11
GCST010701_58	Cortical surface area (MOSTest)	6.000000e-16
GCST010702_152	Subcortical volume (MOSTest)	2.000000e-12
GCST010703_217	Brain morphology (MOSTest)	3.000000e-11
GCST010988_214	Adult body size	5.000000e-08
GCST012361_1	Relative brain age	3.000000e-16
GCST90002381_203	Eosinophil count	2.000000e-131
GCST90002382_593	Eosinophil percentage of white cells	4.000000e-145
GCST90002388_338	Lymphocyte count	1.000000e-11
GCST90002388_339	Lymphocyte count	1.000000e-45
GCST90002389_42	Lymphocyte percentage of white cells	2.000000e-42
GCST90002394_53	Monocyte percentage of white cells	5.000000e-10
GCST90002395_569	Mean platelet volume	5.000000e-15
GCST90002399_418	Neutrophil percentage of white cells	1.000000e-11
GCST90002399_419	Neutrophil percentage of white cells	5.000000e-18

EFO canonical traits (13, from GWAS)

EFO ID	Trait name
EFO:0007991	eosinophil percentage of leukocytes
EFO:0004842	eosinophil count
EFO:0007996	eosinophil percentage of granulocytes
EFO:0007994	neutrophil percentage of granulocytes
EFO:0005090	basophil count
EFO:0004587	lymphocyte count
EFO:0006941	grip strength measurement
EFO:0004346	neuroimaging measurement
EFO:0010602	brain age measurement
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0007989	monocyte percentage of leukocytes
EFO:0007990	neutrophil percentage of leukocytes
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression, increases methylation	6
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
Glupearl 19S	increases expression	1
FR900359	affects phosphorylation	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression, increases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	increases activity, affects binding, decreases expression	1
geraniol	increases expression	1
arsenite	decreases reaction, affects binding	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	affects methylation	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
beta-hydroxy simvastatin acid	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases expression, increases response to substance	1
PCI 5002	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants, Occupational	affects expression	1
Allergens	affects cotreatment, increases abundance, increases expression	1
Vehicle Emissions	affects cotreatment, increases abundance, increases expression	1
Caffeine	affects phosphorylation	1
Formaldehyde	decreases expression	1
Quercetin	decreases expression	1
Silicon Dioxide	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A3Q5	SEES3-1V human KLF3, clone1	Embryonic stem cell	Male
CVCL_A3Q6	SEES3-1V human KLF3, clone2	Embryonic stem cell	Male
CVCL_A3Q7	SEES3-1V human KLF3, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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