SP2

gene
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Also known as KIAA0048

Summary

SP2 (Sp2 transcription factor, HGNC:11207) is a protein-coding gene on chromosome 17q21.32, encoding Transcription factor Sp2 (Q02086). Binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It is a selective cancer dependency (DepMap: 12.7% of cell lines).

This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters.

Source: NCBI Gene 6668 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 82 total
  • Cancer dependency (DepMap): dependent in 12.7% of screened cell lines
  • Transcription factor: yes — 26 downstream targets (CollecTRI)
  • MANE Select transcript: NM_003110

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11207
Approved symbolSP2
NameSp2 transcription factor
Location17q21.32
Locus typegene with protein product
StatusApproved
AliasesKIAA0048
Ensembl geneENSG00000167182
Ensembl biotypeprotein_coding
OMIM601801
Entrez6668

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000376741, ENST00000635868, ENST00000637314, ENST00000637943, ENST00000642065, ENST00000884861, ENST00000884862, ENST00000884863

RefSeq mRNA: 1 — MANE Select: NM_003110 NM_003110

CCDS: CCDS11521

Canonical transcript exons

ENST00000376741 — 7 exons

ExonStartEnd
ENSE000008125634792534847925541
ENSE000009473184792491947925093
ENSE000011375434792296247923274
ENSE000011942714792772447928957
ENSE000014135394791615647917130
ENSE000024496904791531247915388
ENSE000027294064789623647896293

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 92.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1494 / max 105.9616, expressed in 1786 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
16138614.95451784
1613870.194973

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065592.17gold quality
buccal mucosa cellCL:000233692.16gold quality
granulocyteCL:000009488.27gold quality
right testisUBERON:000453488.01gold quality
left testisUBERON:000453387.51gold quality
gastrocnemiusUBERON:000138886.99gold quality
popliteal arteryUBERON:000225086.95gold quality
hindlimb stylopod muscleUBERON:000425286.94gold quality
tibial arteryUBERON:000761086.94gold quality
oocyteCL:000002386.92gold quality
leukocyteCL:000073886.82gold quality
monocyteCL:000057686.68gold quality
mononuclear cellCL:000084286.65gold quality
muscle of legUBERON:000138386.53gold quality
bloodUBERON:000017886.21gold quality
endometrium epitheliumUBERON:000481186.01gold quality
aortaUBERON:000094785.97gold quality
synovial jointUBERON:000221785.93gold quality
right coronary arteryUBERON:000162585.67gold quality
testisUBERON:000047385.63gold quality
right lungUBERON:000216785.52gold quality
vermiform appendixUBERON:000115485.38gold quality
right lobe of thyroid glandUBERON:000111985.36gold quality
left lobe of thyroid glandUBERON:000112085.35gold quality
left uterine tubeUBERON:000130385.29gold quality
descending thoracic aortaUBERON:000234585.25gold quality
thymusUBERON:000237085.19gold quality
parotid glandUBERON:000183185.00silver quality
penisUBERON:000098984.90gold quality
heart left ventricleUBERON:000208484.83gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.58
E-GEOD-100618no67.08

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

26 targets.

TargetRegulation
ALOX15B
CCND1Unknown
CD14Unknown
CDKN1AUnknown
CDKN2A
CEACAM1Repression
CTSLUnknown
DHFRActivation
DNMT3AActivation
DNMT3BActivation
HBB
HSD17B2Repression
KLK3
MAT2AUnknown
MIR638
MMP9Repression
NFATC2Unknown
NFKB
PAPSS1
PAPSS2Unknown
PCYT1ARepression
POLD1
SOCS1
SP1
TFAP2A
TSC1

JASPAR motifs

MotifNameFamily
MA0516.1SP2Three-zinc finger Kruppel-related
MA0516.2SP2Three-zinc finger Kruppel-related
MA0516.3SP2Three-zinc finger Kruppel-related

JASPAR matrix evidence (PMIDs): PMID:22684502, PMID:14726517

Upstream regulators (CollecTRI, top): NFKB, SP1, TFAP2A

miRNA regulators (miRDB)

83 targeting SP2, 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-4283100.0066.422097
HSA-MIR-6851-5P100.0065.631294
HSA-LET-7A-3P100.0074.033932
HSA-MIR-3689D100.0066.141181
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-185-3P99.9567.011743
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-338-5P99.9272.342951
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-61399.9171.501710
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-444799.8567.812900
HSA-MIR-76599.8468.242442
HSA-MIR-473999.8465.251832
HSA-MIR-132199.8465.301811

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 12.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 11)

  • has an intimate part in transcriptional regulation of the lh receptor gene. (PMID:15788387)
  • an SP2/KLF6 repression complex by SHP is required for farnesoid X receptor-induced endothelial cell migration (PMID:17071613)
  • Despite the absence of Sp2 in the 5’-upstream sequence of the human promoter, silencing of Sp2 by RNA interference clearly demonstrated that Sp2 is required for IFN-gamma-induced regulation of socs1 mRNA both in human and mouse. (PMID:19482358)
  • Data show that three Sp1 motifs located between -148 and -42bp upstream of the first exon were important in basic as well as in DA-induced NSMase2 promoter activity. (PMID:19698806)
  • Sp2 is up-regulated in gastric cancer tissues (PMID:24623314)
  • O-GlcNAc modification of Sp3 and Sp4, but not Sp2 transcription factors negatively regulates their transcriptional activities. (PMID:26431879)
  • This study presented that a Novel Mutation (Gly212Val) in the PS2 Gene Associated with Early-Onset Familial Alzheimer’s Disease. (PMID:27128372)
  • SP2 recognized binding motifs in the human RORgammaT promoter, which was critical for maintaining expression. SP2 was necessary for maximum IL-17 expression in in vitro-differentiated Th17 cells. SP 2 plays a role in Th17-dependent physiologic and pathologic immune responses. (PMID:27256574)
  • Sp2 promotes invasion and metastasis of hepatocellular carcinoma by targeting TRIB3 protein. (PMID:32160655)
  • Transcription Factor SP2 Regulates Ski-mediated Astrocyte Proliferation In Vitro. (PMID:34687796)
  • Transcription factor Sp2 promotes TGFB-mediated interstitial cell osteogenic differentiation in bicuspid aortic valves through a SMAD-dependent pathway. (PMID:34914964)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosp2ENSDARG00000076763
mus_musculusSp2ENSMUSG00000018678
rattus_norvegicusSp2ENSRNOG00000010492

Paralogs (3): SP4 (ENSG00000105866), SP3 (ENSG00000172845), SP1 (ENSG00000185591)

Protein

Protein identifiers

Transcription factor Sp2Q02086 (reviewed: Q02086)

All UniProt accessions (5): A0A1B0GTK3, A0A1B0GV29, A0A1B0GVH1, A0A286YFJ7, Q02086

UniProt curated annotations — full annotation on UniProt →

Function. Binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites.

Subcellular location. Nucleus.

Domain organisation. The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors. In SP2, the motif is inactive.

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

Isoforms (2)

UniProt IDNamesCanonical?
Q02086-11yes
Q02086-22

RefSeq proteins (1): NP_003101* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096

UniProt features (13 total): zinc finger region 3, compositionally biased region 3, region of interest 3, chain 1, modified residue 1, splice variant 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q02086-F145.390.00

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 (1): 78

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): CCAWYNNGAAR_UNKNOWN, TGACCTY_ERR1_Q2, GGGTGGRR_PAX4_03, GGAMTNNNNNTCCY_UNKNOWN, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, GCM_RING1, ACATTCC_MIR1_MIR206, MORF_PPP6C, RYTTCCTG_ETS2_B, ACTTTAT_MIR1425P, CUI_TCF21_TARGETS_2_DN, ACEVEDO_LIVER_CANCER_UP, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, TGCCTTA_MIR124A, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN

GO Biological Process (3): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), immune response (GO:0006955)

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 repressor activity, RNA polymerase II-specific (GO:0001227), zinc ion binding (GO:0008270), histone deacetylase binding (GO:0042826), sequence-specific double-stranded DNA binding (GO:1990837), 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:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
regulation of transcription by RNA polymerase II2
transcription by RNA polymerase II2
cellular anatomical structure2
negative regulation of DNA-templated transcription1
regulation of DNA-templated transcription1
immune system process1
response to stimulus1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
transition metal ion binding1
enzyme binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
cation binding1
chromosome1
nuclear lumen1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

576 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SP2POLRMTO00411694
SP2TFB2MQ9H5Q4677
SP2MTERF1Q99551657
SP2TEFMQ96QE5583
SP2TFB1MQ8WVM0582
SP2TFAMQ00059580
SP2MT-ND6P03923542
SP2E2F1Q01094450
SP2MTERF3Q96E29432
SP2FANCD2OSQ96PS1414
SP2MT-CO1P00395400
SP2MT-ND5P03915386
SP2WACQ9BTA9385
SP2ELAC2Q9BQ52379
SP2ZNF263O14978375

IntAct

31 interactions, top by confidence:

ABTypeScore
BANPSP2psi-mi:“MI:0915”(physical association)0.670
FHL2SP2psi-mi:“MI:0915”(physical association)0.670
SP2FHL2psi-mi:“MI:0915”(physical association)0.670
SP2BANPpsi-mi:“MI:0915”(physical association)0.670
MCM7SP2psi-mi:“MI:0915”(physical association)0.560
SP2MCM7psi-mi:“MI:0915”(physical association)0.560
FHL2CNOT1psi-mi:“MI:0914”(association)0.530
VWCEZNF316psi-mi:“MI:0914”(association)0.530
Ppsi-mi:“MI:0914”(association)0.350
SOX2CBX4psi-mi:“MI:0914”(association)0.350
SP1PPP6Cpsi-mi:“MI:0914”(association)0.350
SP2SHTN1psi-mi:“MI:0914”(association)0.350
NOTCH2ZNF320psi-mi:“MI:0914”(association)0.350
TNFRSF1BMAP3K7psi-mi:“MI:0914”(association)0.350
AFG2AESYT2psi-mi:“MI:0914”(association)0.350
AFG2BMMP24OSpsi-mi:“MI:0914”(association)0.350
KLF15ZNF292psi-mi:“MI:2364”(proximity)0.270
SRFZNF292psi-mi:“MI:2364”(proximity)0.270
ELF4SMCHD1psi-mi:“MI:2364”(proximity)0.270
ELK3SMCHD1psi-mi:“MI:2364”(proximity)0.270
FEVTAF4psi-mi:“MI:2364”(proximity)0.270
NFYCASDURFpsi-mi:“MI:2364”(proximity)0.270
GPKOWESYT2psi-mi:“MI:2364”(proximity)0.270
PPIL4ESYT2psi-mi:“MI:2364”(proximity)0.270
ZRANB2SBNO1psi-mi:“MI:2364”(proximity)0.270
NPM1SBNO1psi-mi:“MI:2364”(proximity)0.270

BioGRID (53): SP2 (Two-hybrid), SP2 (Two-hybrid), BANP (Two-hybrid), SP2 (Two-hybrid), SP2 (Two-hybrid), SP2 (Affinity Capture-MS), SP2 (Affinity Capture-MS), SP2 (Affinity Capture-MS), SP2 (Two-hybrid), SP2 (Two-hybrid), SP2 (Two-hybrid), SP2 (Two-hybrid), BANP (Two-hybrid), QRICH1 (Two-hybrid), SP2 (Affinity Capture-Western)

ESM2 similar proteins: A1Z9E2, B0R0I6, B5DE69, G5ED89, O94842, P25425, P32519, P34333, P34447, Q02086, Q08CM4, Q09XV5, Q0IHV2, Q0P5K4, Q0V9U1, Q15723, Q28BL7, Q3TUF7, Q571G4, Q5E9U0, Q5F3U0, Q5R6A9, Q5RBN8, Q5RCV7, Q60775, Q641Z1, Q6DJM6, Q6IQU7, Q6MZP7, Q7Z589, Q7ZUV7, Q7ZX03, Q86NP2, Q8AYC1, Q8BIH0, Q8BMB0, Q8BU11, Q8CHI8, Q8IRW8, Q8WNV2

Diamond homologs: A5ABV9, B5DE03, B7ZSG3, O08584, O08876, O14901, O35738, O35819, O43474, O62259, O62651, O70494, O75840, O89090, O89091, O95600, P08047, P0CG40, P19544, P22561, P46099, P49952, P49953, P50902, P57682, P58334, P79958, Q01714, Q02086, Q02446, Q02447, Q0VA40, Q13118, Q13351, Q13887, Q14V87, Q19A40, Q19A41, Q22678, Q24266

SIGNOR signaling

2 interactions.

AEffectBMechanism
SP2“up-regulates activity”IRF1binding
SP2“down-regulates quantity by repression”PCYT1A“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance71
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1499 predictions. Top by Δscore:

VariantEffectΔscore
17:47896272:G:Tdonor_gain1.0000
17:47896275:G:GTdonor_gain1.0000
17:47896291:GCG:Gdonor_gain1.0000
17:47896343:G:GTdonor_gain1.0000
17:47897794:A:AGacceptor_gain1.0000
17:47897795:A:Gacceptor_gain1.0000
17:47914836:GAT:Gdonor_gain1.0000
17:47922956:TCCCA:Tacceptor_loss1.0000
17:47922957:CCCA:Cacceptor_loss1.0000
17:47922958:CCAG:Cacceptor_loss1.0000
17:47922959:CAG:Cacceptor_loss1.0000
17:47922960:AGG:Aacceptor_loss1.0000
17:47922961:G:GTacceptor_loss1.0000
17:47923231:TGTCC:Tdonor_gain1.0000
17:47923272:GCG:Gdonor_gain1.0000
17:47924908:T:Aacceptor_gain1.0000
17:47924915:ACAG:Aacceptor_gain1.0000
17:47924915:ACAGG:Aacceptor_gain1.0000
17:47924916:C:Gacceptor_gain1.0000
17:47924917:A:AGacceptor_gain1.0000
17:47924917:A:Cacceptor_loss1.0000
17:47924917:AG:Aacceptor_gain1.0000
17:47924917:AGG:Aacceptor_gain1.0000
17:47924918:G:Aacceptor_gain1.0000
17:47924918:G:GGacceptor_gain1.0000
17:47924918:GGG:Gacceptor_gain1.0000
17:47924918:GGGC:Gacceptor_gain1.0000
17:47924918:GGGCA:Gacceptor_gain1.0000
17:47925089:AAGAG:Adonor_loss1.0000
17:47925090:AGAGG:Adonor_loss1.0000

AlphaMissense

3990 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:47925379:T:AC527S1.000
17:47925379:T:CC527R1.000
17:47925380:G:AC527Y1.000
17:47925380:G:CC527S1.000
17:47925381:C:GC527W1.000
17:47925394:T:AC532S1.000
17:47925394:T:CC532R1.000
17:47925395:G:AC532Y1.000
17:47925395:G:CC532S1.000
17:47925396:T:GC532W1.000
17:47925406:T:CF536L1.000
17:47925407:T:CF536S1.000
17:47925408:C:AF536L1.000
17:47925408:C:GF536L1.000
17:47925425:T:CL542P1.000
17:47925463:T:CF555L1.000
17:47925465:T:AF555L1.000
17:47925465:T:GF555L1.000
17:47925469:T:CC557R1.000
17:47925470:G:AC557Y1.000
17:47925471:C:GC557W1.000
17:47925484:T:CC562R1.000
17:47925485:G:AC562Y1.000
17:47925486:T:GC562W1.000
17:47925496:T:CF566L1.000
17:47925497:T:CF566S1.000
17:47925498:C:AF566L1.000
17:47925498:C:GF566L1.000
17:47925515:T:CL572P1.000
17:47925525:T:AH575Q1.000

dbSNP variants (sampled 300 via entrez): RS1000097487 (17:47907147 A>G), RS1000160162 (17:47928874 A>G), RS1000206700 (17:47924371 A>G), RS1000243325 (17:47907140 T>A,C), RS1000289321 (17:47895435 G>A,C), RS1000475640 (17:47926678 T>C), RS1000501187 (17:47895927 G>A), RS1000941023 (17:47913560 T>G), RS1000952242 (17:47913924 A>G), RS1000976505 (17:47920932 C>T), RS1001186601 (17:47913571 C>T), RS1001222480 (17:47906663 C>T), RS1001248237 (17:47906828 G>A), RS1001299627 (17:47906247 A>G), RS1001439079 (17:47906994 C>A,T)

Disease associations

OMIM: gene MIM:601801 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST005146_34Birth weight3.000000e-09
GCST005951_17Body mass index3.000000e-09
GCST006075_22Hair color4.000000e-90
GCST006988_22Blond vs. brown/black hair color9.000000e-16
GCST011457_21Asthma with severe exacerbations8.000000e-07
GCST90002409_45Childhood body mass index8.000000e-07

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004344birth weight
EFO:0004340body mass index
EFO:0003924hair color

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
sodium arseniteincreases expression1
butyraldehydedecreases expression1
tanshinonedecreases expression1
4-hydroxy-2-nonenaldecreases expression1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidineincreases expression, increases response to substance1
jinfukangaffects cotreatment, decreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-oldecreases expression1
Benzo(a)pyrenedecreases methylation1
Cadmiumdecreases expression, increases abundance1
Caffeinedecreases phosphorylation1
Cisplatinaffects cotreatment, decreases expression1
Doxorubicindecreases expression1
Folic Aciddecreases expression1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Urethaneincreases expression1
Valproic Aciddecreases expression1
Cadmium Chloridedecreases expression, increases abundance1
Chlorodiphenyl (54% Chlorine)increases expression1
tert-Butylhydroperoxidedecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_HC93HEK293 eGFP-SP2Transformed cell lineFemale

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): asthma