TSKU

gene
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Also known as E2IG4TSK

Summary

TSKU (tsukushi, small leucine rich proteoglycan, HGNC:28850) is a protein-coding gene on chromosome 11q13.5, encoding Tsukushi (Q8WUA8). Contributes to various developmental events and other processes such as wound healing and cholesterol homeostasis through its interactions with multiple signaling pathways.

Predicted to enable transforming growth factor beta binding activity. Predicted to be involved in several processes, including cholesterol efflux; cholesterol homeostasis; and nervous system development. Predicted to act upstream of or within several processes, including ciliary body morphogenesis; negative regulation of Wnt signaling pathway; and telencephalon development. Predicted to be located in extracellular region. Predicted to be active in extracellular space.

Source: NCBI Gene 25987 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 66 total
  • MANE Select transcript: NM_015516

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28850
Approved symbolTSKU
Nametsukushi, small leucine rich proteoglycan
Location11q13.5
Locus typegene with protein product
StatusApproved
AliasesE2IG4, TSK
Ensembl geneENSG00000182704
Ensembl biotypeprotein_coding
OMIM608015
Entrez25987

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 16 protein_coding

ENST00000333090, ENST00000525167, ENST00000527881, ENST00000533752, ENST00000612930, ENST00000870292, ENST00000870293, ENST00000870294, ENST00000870295, ENST00000870296, ENST00000870297, ENST00000870298, ENST00000870299, ENST00000870300, ENST00000956905, ENST00000956906

RefSeq mRNA: 5 — MANE Select: NM_015516 NM_001258210, NM_001318477, NM_001318478, NM_001318479, NM_015516

CCDS: CCDS8246

Canonical transcript exons

ENST00000333090 — 2 exons

ExonStartEnd
ENSE000013047987678335676783404
ENSE000022012197679560976798144

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 98.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.4636 / max 314.7449, expressed in 1588 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1159629.17461552
1159637.04571254
2063920.145546
1159590.097748

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
deciduaUBERON:000245098.50gold quality
endocervixUBERON:000045897.89gold quality
ectocervixUBERON:001224997.56gold quality
left uterine tubeUBERON:000130395.72gold quality
mucosa of stomachUBERON:000119995.50gold quality
right lobe of liverUBERON:000111495.20gold quality
lower esophagus mucosaUBERON:003583494.78gold quality
subcutaneous adipose tissueUBERON:000219094.63gold quality
vaginaUBERON:000099694.21gold quality
skin of abdomenUBERON:000141694.00gold quality
tibial nerveUBERON:000132393.73gold quality
skin of legUBERON:000151193.48gold quality
vena cavaUBERON:000408793.40gold quality
mammalian vulvaUBERON:000099793.32gold quality
liverUBERON:000210793.30gold quality
esophagus mucosaUBERON:000246993.23gold quality
omental fat padUBERON:001041492.96gold quality
peritoneumUBERON:000235892.94gold quality
adipose tissue of abdominal regionUBERON:000780892.87gold quality
adipose tissueUBERON:000101392.84gold quality
zone of skinUBERON:000001492.42gold quality
olfactory segment of nasal mucosaUBERON:000538692.28gold quality
right ovaryUBERON:000211892.07gold quality
connective tissueUBERON:000238491.88gold quality
uterine cervixUBERON:000000291.56gold quality
left coronary arteryUBERON:000162691.51gold quality
coronary arteryUBERON:000162191.28gold quality
right lobe of thyroid glandUBERON:000111991.26gold quality
synovial jointUBERON:000221790.97gold quality
left lobe of thyroid glandUBERON:000112090.95gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-CURD-10no110.07
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

90 targeting TSKU, 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-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-3163100.0077.238605
HSA-MIR-366299.9973.825684
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-211099.9666.681930
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-96-5P99.9572.802140
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-452599.9464.38675
HSA-MIR-1213399.9271.822006
HSA-MIR-1271-5P99.9171.991972
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-17-5P99.8973.832665
HSA-MIR-427199.8868.322244
HSA-MIR-605-3P99.8869.221833
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607

Literature-anchored findings (GeneRIF, showing 9)

  • The spatio-temporal expression of Decorin, Semaphorin6D, SPARC, Spry-1 and Tsukushi in developing prostate is described and observed similar mesenchymal expression patterns in rat and human. (PMID:22880013)
  • TSK controls the hair cycle by regulating TGF-beta1 signaling. (PMID:22995554)
  • Among its predicted target genes down-regulated by miR-2110, knockdown of Tsukushi (TSKU) expression showed the most potent effect in inducing cell differentiation and reducing cell survival, suggesting that TSKU protein plays a key role in mediating the functions of miR-2110. Low tumor miR-2110 levels were significantly correlated with high tumor TSKU mRNA levels. (PMID:30550571)
  • in lung cancer cells, TSK is expressed more highly than the other small leucine-rich repeat proteoglycan family members, and regulates the epithelial-mesenchymal transition and cell proliferation (PMID:31027686)
  • The hepatokine Tsukushi is released in response to NAFLD and impacts cholesterol homeostasis. (PMID:31391339)
  • Gastric banding-associated weight loss diminishes hepatic Tsukushi expression. (PMID:32442908)
  • Elevated Serum Tsukushi Levels in Patients With Hyperthyroidism. (PMID:33117292)
  • Novel roles of Tsukushi in signaling pathways and multiple disease processes. (PMID:33759220)
  • Tsukushi and TSKU genotype in obesity and related metabolic disorders. (PMID:33860453)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotskuENSDARG00000040815
mus_musculusTskuENSMUSG00000049580
rattus_norvegicusTskuENSRNOG00000027784

Paralogs (22): IGFALS (ENSG00000099769), TLR8 (ENSG00000101916), LRRC17 (ENSG00000128606), RXFP2 (ENSG00000133105), CD180 (ENSG00000134061), TLR4 (ENSG00000136869), TLR2 (ENSG00000137462), LRRC32 (ENSG00000137507), LRRC3 (ENSG00000160233), LRRC53 (ENSG00000162621), TLR3 (ENSG00000164342), VASN (ENSG00000168140), RXFP1 (ENSG00000171509), NRROS (ENSG00000174004), TLR10 (ENSG00000174123), TLR1 (ENSG00000174125), TLR6 (ENSG00000174130), LRRC3B (ENSG00000179796), TLR5 (ENSG00000187554), TLR7 (ENSG00000196664), LRIT2 (ENSG00000204033), LRRC3C (ENSG00000204913)

Protein

Protein identifiers

TsukushiQ8WUA8 (reviewed: Q8WUA8)

Alternative names: E2-induced gene 4 protein, Leucine-rich repeat-containing protein 54

All UniProt accessions (3): Q8WUA8, E9PLG7, E9PN12

UniProt curated annotations — full annotation on UniProt →

Function. Contributes to various developmental events and other processes such as wound healing and cholesterol homeostasis through its interactions with multiple signaling pathways. Wnt signaling inhibitor which competes with WNT2B for binding to Wnt receptor FZD4 and represses WNT2B-dependent development of the peripheral eye. Plays a role in regulating the hair cycle by controlling TGFB1 signaling. Required for the development of the anterior commissure in the brain by inhibiting neurite outgrowth. Essential for terminal differentiation of hippocampal neural stem cells. Plays a role in regulating bone elongation and bone mass by modulating growth plate chondrocyte function and overall body size. Required for development of the inner ear through its involvement in stereocilia formation in inner hair cells. Facilitates wound healing by inhibiting secretion of TGFB1 from macrophages which prevents myofibroblast differentiation, maintaining inflammatory cell quiescence. Plays a role in cholesterol homeostasis by reducing circulating high-density lipoprotein cholesterol, lowering cholesterol efflux capacity and decreasing cholesterol-to-bile acid conversion in the liver. In one study, shown to negatively regulate sympathetic innervation in brown fat, leading to reduced energy expenditure. In another study, shown not to affect brown fat thermogenic capacity, body weight gain or glucose homeostasis.

Subunit / interactions. Interacts with FZD4 (via FZ domain); competes with WNT2B for binding to FZD4, inhibiting Wnt signaling and repressing peripheral eye development. Interacts with TGFB1; the interaction contributes to regulation of the hair cycle. Interacts with netrin. Interacts with CCN2.

Subcellular location. Secreted.

Induction. By 17-beta-estradiol.

Miscellaneous. This factor is named ‘Tsukushi’ because its expression pattern in chick embryos is similar to the shape of the Japanese horsetail plant, tsukushi.

RefSeq proteins (5): NP_001245139, NP_001305406, NP_001305407, NP_001305408, NP_056331* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR032675LRR_dom_sfHomologous_superfamily

Pfam: PF00560, PF13855

UniProt features (20 total): repeat 10, sequence variant 4, glycosylation site 2, signal peptide 1, chain 1, sequence conflict 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WUA8-F186.550.62

Functional residue map

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

Glycosylation sites (2): 74, 137

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 257 (showing top): GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_STEROL_HOMEOSTASIS, GOBP_GROWTH, GOBP_NEUROGENESIS, TAL1ALPHAE47_01, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_CHONDROCYTE_DEVELOPMENT, GOBP_REGULATION_OF_HAIR_CYCLE, CAGGTCC_MIR492, GOBP_VENTRICULAR_SYSTEM_DEVELOPMENT, GOBP_BONE_GROWTH, chr11q13, GOBP_FOREBRAIN_DEVELOPMENT, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT

GO Biological Process (24): growth plate cartilage chondrocyte development (GO:0003431), immune response (GO:0006955), transforming growth factor beta receptor signaling pathway (GO:0007179), cholesterol metabolic process (GO:0008203), regulation of gene expression (GO:0010468), negative regulation of neuron projection development (GO:0010977), corpus callosum morphogenesis (GO:0021540), lateral ventricle development (GO:0021670), hippocampus development (GO:0021766), anterior commissure morphogenesis (GO:0021960), negative regulation of Wnt signaling pathway (GO:0030178), negative regulation of transforming growth factor beta1 production (GO:0032911), cholesterol efflux (GO:0033344), wound healing (GO:0042060), cholesterol homeostasis (GO:0042632), positive regulation of hair cycle (GO:0042635), camera-type eye development (GO:0043010), inner ear receptor cell stereocilium organization (GO:0060122), ciliary body morphogenesis (GO:0061073), energy homeostasis (GO:0097009), bone growth (GO:0098868), negative regulation of myofibroblast differentiation (GO:1904761), nervous system development (GO:0007399), anatomical structure morphogenesis (GO:0009653)

GO Molecular Function (3): transforming growth factor beta binding (GO:0050431), protein binding (GO:0005515), cytokine binding (GO:0019955)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
neuron projection development2
central nervous system projection neuron axonogenesis2
telencephalon development2
anatomical structure development2
growth plate cartilage chondrocyte differentiation1
chondrocyte development involved in endochondral bone morphogenesis1
immune system process1
response to stimulus1
cellular response to transforming growth factor beta stimulus1
transforming growth factor beta receptor superfamily signaling pathway1
sterol metabolic process1
secondary alcohol metabolic process1
gene expression1
regulation of macromolecule biosynthetic process1
regulation of neuron projection development1
negative regulation of cell projection organization1
corpus callosum development1
ventricular system development1
pallium development1
limbic system development1
negative regulation of signal transduction1
Wnt signaling pathway1
regulation of Wnt signaling pathway1
transforming growth factor beta1 production1
regulation of transforming growth factor beta1 production1
negative regulation of transforming growth factor beta production1
cholesterol transport1
response to wounding1
tissue regeneration1
sterol homeostasis1
hair cycle1
regulation of hair cycle1
positive regulation of multicellular organismal process1
eye development1
inner ear receptor cell development1
anatomical structure morphogenesis1
camera-type eye morphogenesis1
multicellular organismal-level homeostasis1
growth factor binding1
cytokine binding1

Protein interactions and networks

STRING

1016 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TSKUCHRDQ9H2X0834
TSKUFZD4Q9ULV1710
TSKUACER3Q9NUN7542
TSKUCCDC201A0A1B0GTI1526
TSKUBMP4P12644492
TSKUTGFB1P01137478
TSKUFGF8P55075470
TSKUD6RC18D6RC18459
TSKUPDE4CQ08493459
TSKUZSCAN2Q7Z7L9454
TSKUOPTCQ9UBM4445
TSKUTBRG1Q3YBR2439
TSKUSTOML1Q9UBI4425
TSKUEPDR1Q9UM22406
TSKUOMDQ99983404

IntAct

8 interactions, top by confidence:

ABTypeScore
SKILTSKUpsi-mi:“MI:0915”(physical association)0.370
UXS1IPO7psi-mi:“MI:0914”(association)0.350
SHTN1psi-mi:“MI:0914”(association)0.350
UXS1HRASpsi-mi:“MI:0914”(association)0.350
UXS1PDE2Apsi-mi:“MI:0914”(association)0.350
SLC30A5NBASpsi-mi:“MI:0914”(association)0.350

BioGRID (9): TSKU (Affinity Capture-MS), TSKU (Affinity Capture-MS), TSKU (Affinity Capture-MS), TSKU (Proximity Label-MS), TSKU (Protein-peptide), TSKU (Affinity Capture-MS), TSKU (Cross-Linking-MS (XL-MS)), TSKU (Affinity Capture-MS), TSKU (Two-hybrid)

ESM2 similar proteins: A1A4H9, A4IFA6, A6NDA9, E7FE13, G3XA59, O08644, O08742, O08770, O14498, O15197, P0C0K6, P0C0K7, P35590, P40197, P59383, Q06805, Q06806, Q14392, Q149C3, Q3ZBI5, Q5JZY3, Q5NVQ6, Q5R6B1, Q5RF01, Q5RKR3, Q6EMK4, Q6GU68, Q6P7C4, Q6PFC5, Q6QMY6, Q6UXK2, Q6UY18, Q80ZD5, Q86UE6, Q86WK7, Q86YC3, Q8BGX3, Q8BYG9, Q8C2S7, Q8CBR6

Diamond homologs: A3KNN3, A4IFA6, A4IIW9, A6H789, A6H793, A6NJW4, A8WHP9, C3YZ59, E5DHB5, F7D3V9, G5EFX6, O14498, O35367, O46542, O60938, O62702, O75093, O75094, O75473, O88186, O88279, O88280, O94813, P07585, P14770, P21793, P24014, P28654, P28675, P59034, P59035, P70193, Q01129, Q13641, Q28888, Q29393, Q3SXY7, Q3ZBN5, Q45R42, Q4KLL3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance58
Likely benign6
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

356 predictions. Top by Δscore:

VariantEffectΔscore
11:76795607:A:AGacceptor_gain1.0000
11:76795608:G:GGacceptor_gain1.0000
11:76793801:GGG:Gdonor_gain0.9900
11:76793802:GGG:Gdonor_gain0.9900
11:76795603:TTCTA:Tacceptor_loss0.9900
11:76795604:TCTA:Tacceptor_loss0.9900
11:76795605:CTA:Cacceptor_loss0.9900
11:76795606:TAG:Tacceptor_loss0.9900
11:76795608:G:Aacceptor_loss0.9900
11:76793803:G:Tdonor_gain0.9800
11:76795608:GC:Gacceptor_gain0.9800
11:76795608:GCC:Gacceptor_gain0.9800
11:76795608:GCCC:Gacceptor_gain0.9800
11:76795608:GCCCC:Gacceptor_gain0.9800
11:76782430:CAAG:Cdonor_loss0.9700
11:76782431:AAGG:Adonor_loss0.9700
11:76782433:GGTA:Gdonor_loss0.9700
11:76793798:A:Tdonor_gain0.9700
11:76783404:GGT:Gdonor_loss0.9500
11:76783405:G:Tdonor_loss0.9500
11:76783406:T:Gdonor_loss0.9500
11:76784707:GA:Gdonor_gain0.9500
11:76784708:A:Gdonor_gain0.9300
11:76792409:T:Gdonor_gain0.9100
11:76792701:C:Aacceptor_gain0.9100
11:76782835:T:TAdonor_gain0.8900
11:76782836:A:AAdonor_gain0.8900
11:76784653:G:GTdonor_gain0.8900
11:76783407:GAGT:Gdonor_loss0.8800
11:76793752:G:GTacceptor_gain0.8700

AlphaMissense

2240 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:76795888:T:CL91P0.993
11:76795725:T:CF37L0.992
11:76795727:C:AF37L0.992
11:76795727:C:GF37L0.992
11:76795747:G:AC44Y0.992
11:76795748:T:GC44W0.991
11:76795804:T:CL63S0.991
11:76795746:T:AC44S0.989
11:76795747:G:CC44S0.989
11:76795810:T:CL65P0.989
11:76795898:C:AN94K0.989
11:76795898:C:GN94K0.989
11:76795960:T:CL115P0.989
11:76795692:T:AC26S0.987
11:76795693:G:CC26S0.987
11:76795746:T:CC44R0.987
11:76795882:T:CL89P0.987
11:76795888:T:AL91H0.987
11:76795686:T:AC24S0.986
11:76795687:G:CC24S0.986
11:76796117:C:AN167K0.986
11:76796117:C:GN167K0.986
11:76796029:T:CL138P0.985
11:76795717:T:GF34C0.984
11:76795722:A:CS36R0.984
11:76795724:C:AS36R0.984
11:76795724:C:GS36R0.984
11:76795954:T:AL113H0.984
11:76795716:T:CF34L0.983
11:76795718:C:AF34L0.983

dbSNP variants (sampled 300 via entrez): RS1000116931 (11:76783363 C>T), RS1000204734 (11:76788733 T>C), RS1000352507 (11:76795280 C>T), RS1000629388 (11:76794623 C>G), RS1000861856 (11:76784495 C>T), RS1000923587 (11:76790075 A>G), RS1001016704 (11:76789714 T>A,C,G), RS1001103322 (11:76784131 C>A,T), RS1001209889 (11:76790233 A>G), RS1001245882 (11:76785442 G>A), RS1001467160 (11:76797480 G>A,C), RS1001756036 (11:76796401 C>A,T), RS1002041133 (11:76780733 G>A,C), RS1002096572 (11:76780435 T>C), RS1002097601 (11:76785282 A>C)

Disease associations

OMIM: gene MIM:608015 | 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
GCST007401_26Factor VII activity1.000000e-10
GCST007401_7Factor VII activity2.000000e-10
GCST009798_77Asthma4.000000e-35
GCST009798_82Asthma2.000000e-45
GCST010988_422Adult body size5.000000e-08
GCST90000514_17Gastroesophageal reflux disease1.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004619factor VII measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, increases expression8
Estradiolaffects reaction, increases reaction, decreases reaction, increases expression, decreases expression (+1 more)5
Tetrachlorodibenzodioxindecreases expression, increases expression, affects expression, affects binding, increases reaction5
bisphenol Aincreases expression, affects expression4
sodium arseniteincreases abundance, increases expression, decreases expression3
Genisteinincreases expression3
graphene oxideincreases expression2
Rifampinincreases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Cyclosporinedecreases expression, increases expression2
Aflatoxin B1affects expression, decreases expression2
aristolochic acid Idecreases expression1
pirinixic acidaffects binding, increases activity, increases expression1
tris(2-butoxyethyl) phosphateaffects expression1
o,p’-DDTincreases expression1
afimoxifenedecreases reaction, increases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydedecreases expression1
9,10-dihydro-9,10-dihydroxybenzo(a)pyreneincreases expression1
beta-methylcholineaffects expression1
brequinarincreases expression1
CGP 52608affects binding, increases reaction1
chloropicrindecreases expression1
corosolic acidincreases expression1
ICG 001increases expression1
abrinedecreases expression1
jinfukangaffects cotreatment, increases expression1
picoxystrobindecreases expression1
(+)-JQ1 compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases 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): gastroesophageal reflux disease