STMN3

gene
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Also known as SCLIP

Summary

STMN3 (stathmin 3, HGNC:15926) is a protein-coding gene on chromosome 20q13.33, encoding Stathmin-3 (Q9NZ72). Exhibits microtubule-destabilizing activity, which is antagonized by STAT3.

This gene encodes a protein which is a member of the stathmin protein family. Members of this protein family form a complex with tubulins at a ratio of 2 tubulins for each stathmin protein. Microtubules require the ordered assembly of alpha- and beta-tubulins, and formation of a complex with stathmin disrupts microtubule formation and function. A pseudogene of this gene is located on chromosome 22. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 50861 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 26 total
  • MANE Select transcript: NM_015894

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15926
Approved symbolSTMN3
Namestathmin 3
Location20q13.33
Locus typegene with protein product
StatusApproved
AliasesSCLIP
Ensembl geneENSG00000197457
Ensembl biotypeprotein_coding
OMIM608362
Entrez50861

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 9 protein_coding

ENST00000370053, ENST00000540534, ENST00000631920, ENST00000632676, ENST00000634126, ENST00000860150, ENST00000860151, ENST00000940055, ENST00000953346

RefSeq mRNA: 2 — MANE Select: NM_015894 NM_001276310, NM_015894

CCDS: CCDS13529, CCDS63330

Canonical transcript exons

ENST00000370053 — 5 exons

ExonStartEnd
ENSE000014516316363971263641397
ENSE000014516396365332763653424
ENSE000017629026364210863642299
ENSE000036857176364421463644309
ENSE000037879186364375663643931

Expression profiles

Bgee: expression breadth ubiquitous, 230 present calls, max score 99.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 59.7891 / max 1604.5738, expressed in 1571 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
18840148.11601517
1884026.68741195
1884003.83321015
1883960.387884
1883950.277566
1884040.2750136
1884030.138781
1883940.073641

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ponsUBERON:000098899.59gold quality
right frontal lobeUBERON:000281099.24gold quality
middle temporal gyrusUBERON:000277199.15gold quality
Brodmann (1909) area 23UBERON:001355499.15gold quality
right hemisphere of cerebellumUBERON:001489099.14gold quality
lateral nuclear group of thalamusUBERON:000273699.12gold quality
endothelial cellCL:000011599.07gold quality
cerebellar hemisphereUBERON:000224599.06gold quality
cerebellar cortexUBERON:000212999.05gold quality
primary visual cortexUBERON:000243699.00gold quality
anterior cingulate cortexUBERON:000983598.97gold quality
superior vestibular nucleusUBERON:000722798.95gold quality
nucleus accumbensUBERON:000188298.87gold quality
entorhinal cortexUBERON:000272898.80gold quality
cingulate cortexUBERON:000302798.77gold quality
parietal lobeUBERON:000187298.71gold quality
cerebellar vermisUBERON:000472098.67gold quality
postcentral gyrusUBERON:000258198.63gold quality
temporal lobeUBERON:000187198.50gold quality
caudate nucleusUBERON:000187398.41gold quality
substantia nigra pars compactaUBERON:000196598.41gold quality
ventral tegmental areaUBERON:000269198.38gold quality
lateral globus pallidusUBERON:000247698.35gold quality
amygdalaUBERON:000187698.31gold quality
prefrontal cortexUBERON:000045198.29gold quality
dorsal root ganglionUBERON:000004498.15gold quality
cerebellumUBERON:000203798.08gold quality
substantia nigra pars reticulataUBERON:000196697.91gold quality
dorsolateral prefrontal cortexUBERON:000983497.89gold quality
neocortexUBERON:000195097.87gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-MTAB-7316yes14.64
E-HCAD-25yes9.41
E-HCAD-10yes4.93
E-ANND-3yes4.03
E-GEOD-36552no216.38
E-GEOD-110499no28.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting STMN3, 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-4455100.0065.481587
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-569899.9768.492029
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-185-3P99.9567.011743
HSA-MIR-452599.9464.38675
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-579-3P99.8671.663628
HSA-MIR-444799.8567.812900
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-431999.7669.832586
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-1255A99.7468.09744
HSA-MIR-1255B-5P99.7468.16741
HSA-MIR-447299.5666.081478
HSA-MIR-448999.5065.56785
HSA-MIR-127599.4767.902749
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-302A-5P99.3968.211913
HSA-MIR-6853-3P99.3670.791558
HSA-MIR-429299.1665.571767
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-6769B-5P98.7364.911092
HSA-MIR-6776-5P98.5467.431304
HSA-MIR-430597.9468.63533

Literature-anchored findings (GeneRIF, showing 8)

  • The substantial expression of SCLIP in most tissues points out a novel function outside the nervous system and raises the possibility that its coexpression with stathmin could provide some degree of functional redundancy. (PMID:12676564)
  • SCLIP and SCG10 were colocalized to the Golgi apparatus of chromaffin cells in vivo and shared localization with CHGA as it transited the Golgi. (PMID:18549247)
  • Studies suggest that a STAT3-SCLIP interaction is required to preserve SCLIP stability and contributes to the maintenance of normal epithelial morphology. (PMID:19824884)
  • Specific serine-proline phosphorylation and glycogen synthase kinase 3beta-directed subcellular targeting of stathmin 3/Sclip in neurons (PMID:22577147)
  • We found that reduced expression and possibly posttranslational modification of SCLIP following paclitaxel treatment impaired the microtubule-destabilizing effect of SCLIP (PMID:23543364)
  • STMN and SCG10 are similarly targeted by JNK but there are clear differences in JNK recognition and phosphorylation of the closely related family member, SCLIP. (PMID:24589734)
  • Overexpression of ID1 in two different cell lines induced STMN3 and GSPT1 at the transcriptional level, while depletion of ID1 reduced their expression. (PMID:25028095)
  • our findings demonstrate that SCLIP plays an important role in glioma pathology, and may represent a novel therapeutic strategy against human glioma. (PMID:25511414)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriostmn3ENSDARG00000038465
mus_musculusStmn3ENSMUSG00000027581
rattus_norvegicusStmn3ENSRNOG00000013657
drosophila_melanogasterstaiFBGN0266521

Paralogs (4): STMN4 (ENSG00000015592), STMN2 (ENSG00000104435), STMN1 (ENSG00000117632), STMND1 (ENSG00000230873)

Protein

Protein identifiers

Stathmin-3Q9NZ72 (reviewed: Q9NZ72)

Alternative names: SCG10-like protein

All UniProt accessions (3): A0A0J9YW36, A0A0J9YXY4, Q9NZ72

UniProt curated annotations — full annotation on UniProt →

Function. Exhibits microtubule-destabilizing activity, which is antagonized by STAT3.

Subunit / interactions. Interacts with STAT3. Interacts with CLU (secreted form); this interaction may act as an important modulator during neuronal differentiation.

Subcellular location. Golgi apparatus. Cell projection. Growth cone. Axon. Cytoplasm. Cytosol.

Tissue specificity. Neuron specific.

Post-translational modifications. N-terminal palmitoylation promotes specific anchoring to the cytosolic leaflet of Golgi membranes and subsequent vesicular trafficking along dendrites and axons. Neuronal Stathmins are substrates for palmitoyltransferases ZDHHC3, ZDHHC7 and ZDHHC15.

Similarity. Belongs to the stathmin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NZ72-11yes
Q9NZ72-22

RefSeq proteins (2): NP_001263239, NP_056978* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000956Stathmin_famFamily
IPR030514Stathmin_CSConserved_site
IPR036002Stathmin_sfHomologous_superfamily

Pfam: PF00836

UniProt features (16 total): modified residue 7, lipid moiety-binding region 2, chain 1, domain 1, splice variant 1, sequence conflict 1, region of interest 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NZ72-F185.850.61

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 (9): 73, 81, 22, 24, 50, 60, 65, 68, 72

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 219 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOZGIT_ESR1_TARGETS_DN, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_NEUROGENESIS, GOBP_NEGATIVE_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, GOBP_MICROTUBULE_DEPOLYMERIZATION

GO Biological Process (9): blastocyst hatching (GO:0001835), microtubule depolymerization (GO:0007019), nervous system development (GO:0007399), negative regulation of neuron projection development (GO:0010977), regulation of microtubule polymerization or depolymerization (GO:0031110), cytoplasmic microtubule organization (GO:0031122), neuron projection development (GO:0031175), negative regulation of Rac protein signal transduction (GO:0035021), regulation of cytoskeleton organization (GO:0051493)

GO Molecular Function (3): tubulin binding (GO:0015631), protein domain specific binding (GO:0019904), protein binding (GO:0005515)

GO Cellular Component (7): cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), cytosol (GO:0005829), growth cone (GO:0030426), neuron projection (GO:0043005), axon (GO:0030424), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
microtubule polymerization or depolymerization2
supramolecular fiber organization2
cytoplasm2
blastocyst development1
hatching1
protein depolymerization1
system development1
regulation of neuron projection development1
neuron projection development1
negative regulation of cell projection organization1
regulation of microtubule cytoskeleton organization1
microtubule cytoskeleton organization1
neuron development1
plasma membrane bounded cell projection organization1
Rac protein signal transduction1
regulation of Rac protein signal transduction1
negative regulation of small GTPase mediated signal transduction1
cytoskeleton organization1
regulation of organelle organization1
cytoskeletal protein binding1
protein binding1
binding1
intracellular anatomical structure1
endomembrane system1
intracellular membrane-bounded organelle1
site of polarized growth1
distal axon1
plasma membrane bounded cell projection1
neuron projection1

Protein interactions and networks

STRING

1980 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STMN3ZGPATQ8N5A5523
STMN3GMEB2Q9UKD1515
STMN3C2orf80Q0P641498
STMN3ARFRP1Q13795472
STMN3LIME1Q9H400431
STMN3FNDC11Q9BVV2418
STMN3SLC2A4RGQ9NR83385
STMN3GNG3P29798380
STMN3RTEL1Q9NZ71374
STMN3HOXA2O43364372
STMN3LRPAP1P30533370
STMN3TMEM239Q8WW34360
STMN3ARPC3O15145352
STMN3SV2AQ7L0J3351
STMN3SLC1A2P43004350

IntAct

94 interactions, top by confidence:

ABTypeScore
UBA7ISG15psi-mi:“MI:0914”(association)0.890
PKN1STMN3psi-mi:“MI:0915”(physical association)0.560
CTNNA3STMN3psi-mi:“MI:0915”(physical association)0.560
ENKD1STMN3psi-mi:“MI:0915”(physical association)0.560
KRT34STMN3psi-mi:“MI:0915”(physical association)0.560
MIPOL1STMN3psi-mi:“MI:0915”(physical association)0.560
STMN3CTNNA3psi-mi:“MI:0915”(physical association)0.560
CARD9STMN3psi-mi:“MI:0915”(physical association)0.560
HGSSTMN3psi-mi:“MI:0915”(physical association)0.560
STMN3ANKRD11psi-mi:“MI:0915”(physical association)0.560
SMARCD1STMN3psi-mi:“MI:0915”(physical association)0.560
TRIM69STMN3psi-mi:“MI:0915”(physical association)0.560
TXLNBSTMN3psi-mi:“MI:0915”(physical association)0.560
KAT5STMN3psi-mi:“MI:0915”(physical association)0.560
POLR1CSTMN3psi-mi:“MI:0915”(physical association)0.560
GPANK1STMN3psi-mi:“MI:0915”(physical association)0.560
KIFC3STMN3psi-mi:“MI:0915”(physical association)0.560
AIRIMSTMN3psi-mi:“MI:0915”(physical association)0.560
PLEKHA7STMN3psi-mi:“MI:0915”(physical association)0.560
ZNF76STMN3psi-mi:“MI:0915”(physical association)0.560
MKRN3STMN3psi-mi:“MI:0915”(physical association)0.560
EXOC8STMN3psi-mi:“MI:0915”(physical association)0.560
P4HA3STMN3psi-mi:“MI:0915”(physical association)0.560

BioGRID (48): STMN3 (Two-hybrid), TRPC5 (Reconstituted Complex), STMN3 (Affinity Capture-RNA), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid), STMN3 (Two-hybrid)

ESM2 similar proteins: A0A088MLT8, A2AQ19, A4FV29, A4IFK9, B3KU38, O14795, O70166, O93388, O95983, P21818, P31395, P50751, P54227, P55821, P63042, P63043, Q09001, Q09002, Q09004, Q09006, Q2KJ58, Q32L68, Q4KUS2, Q4R4N5, Q5F3L9, Q5FVJ5, Q5PSV4, Q5R4C5, Q5R562, Q5R8C6, Q5RAD5, Q62768, Q6GQB5, Q8IVM0, Q8IW50, Q8TBN0, Q8VDV3, Q90987, Q92541, Q93045

Diamond homologs: A4IFK9, A9YWH3, O70166, O93388, P13668, P16949, P21818, P31395, P54227, P55821, P63042, P63043, Q09001, Q09002, Q09004, Q09005, Q09006, Q3T0C7, Q4R4N5, Q4R712, Q5R4C5, Q5R8C6, Q6DUB7, Q90987, Q93045, Q9H169, Q9JHU6, Q9NZ72

SIGNOR signaling

6 interactions.

AEffectBMechanism
GSK3B“up-regulates activity”STMN3phosphorylation
GSK3A“up-regulates activity”STMN3phosphorylation
CDK5unknownSTMN3phosphorylation
MAPK1unknownSTMN3phosphorylation
STMN3“down-regulates quantity by destabilization”Microtubule_polimerizationbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance22
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

793 predictions. Top by Δscore:

VariantEffectΔscore
20:63643749:T:TAdonor_gain1.0000
20:63643758:T:TAdonor_gain1.0000
20:63643927:CATGT:Cacceptor_gain1.0000
20:63643929:TGT:Tacceptor_gain1.0000
20:63643930:GT:Gacceptor_gain1.0000
20:63643931:TC:Tacceptor_loss1.0000
20:63643932:C:CCacceptor_gain1.0000
20:63644212:AC:Adonor_gain1.0000
20:63644212:ACC:Adonor_gain1.0000
20:63644212:ACCC:Adonor_gain1.0000
20:63644213:CC:Cdonor_gain1.0000
20:63644213:CCC:Cdonor_gain1.0000
20:63644213:CCCC:Cdonor_gain1.0000
20:63644305:GTAGG:Gacceptor_gain1.0000
20:63644306:TAGG:Tacceptor_gain1.0000
20:63644310:C:CCacceptor_gain1.0000
20:63642296:GCGT:Gacceptor_gain0.9900
20:63642297:CGT:Cacceptor_gain0.9900
20:63642297:CGTC:Cacceptor_gain0.9900
20:63642300:C:CCacceptor_gain0.9900
20:63642300:C:CGacceptor_loss0.9900
20:63643928:ATGT:Aacceptor_gain0.9900
20:63644207:CACT:Cdonor_loss0.9900
20:63644208:ACTC:Adonor_loss0.9900
20:63644209:CTCA:Cdonor_loss0.9900
20:63644210:TCAC:Tdonor_loss0.9900
20:63644211:C:CGdonor_loss0.9900
20:63644212:A:ACdonor_gain0.9900
20:63644212:A:Cdonor_loss0.9900
20:63644213:C:Adonor_loss0.9900

AlphaMissense

1173 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:63643885:G:CF54L0.999
20:63643885:G:TF54L0.999
20:63643887:A:GF54L0.999
20:63642146:C:GA149P0.998
20:63642184:A:GL136P0.998
20:63643759:C:AR96S0.998
20:63643759:C:GR96S0.998
20:63643763:C:GR95P0.998
20:63641375:C:GR169P0.997
20:63642118:A:GL158P0.997
20:63643773:C:GA92P0.997
20:63643886:A:GF54S0.997
20:63642121:C:GR157P0.996
20:63642134:C:GA153P0.996
20:63642151:C:GR147P0.996
20:63642197:C:GA132P0.996
20:63643880:A:TV56D0.996
20:63643895:C:TG51D0.996
20:63642130:A:GL154P0.995
20:63642139:A:GL151P0.995
20:63642259:C:GR111P0.995
20:63643760:C:GR96T0.995
20:63644265:A:GC22R0.994
20:63641376:G:TR169S0.993
20:63643874:A:GL58P0.993
20:63644259:A:GC24R0.993
20:63641388:C:GA165P0.992
20:63642230:C:GA121P0.992
20:63642269:C:GA108P0.992
20:63642271:A:GL107P0.992

dbSNP variants (sampled 300 via entrez): RS1000121665 (20:63639726 G>A), RS1000320928 (20:63653432 A>G), RS1000440240 (20:63651561 G>A,C), RS1000567247 (20:63644729 A>T), RS1000619377 (20:63649803 T>A,C,G), RS1000720345 (20:63650065 T>A), RS1000915752 (20:63646079 C>T), RS1000970154 (20:63652610 G>A), RS1001131006 (20:63639350 C>A,G), RS1001397739 (20:63655384 T>C), RS1001540286 (20:63650579 A>C,G), RS1001616076 (20:63647115 C>T), RS1001838230 (20:63649336 C>T), RS1001949441 (20:63649686 A>G), RS1002111843 (20:63655288 CAT>C)

Disease associations

OMIM: gene MIM:608362 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST000964_24Ulcerative colitis2.000000e-10
GCST001942_22Prostate cancer4.000000e-16
GCST004131_34Inflammatory bowel disease3.000000e-26
GCST004132_110Crohn’s disease3.000000e-13
GCST004133_15Ulcerative colitis9.000000e-17
GCST007563_15Allergic disease (asthma, hay fever or eczema)3.000000e-08
GCST007564_6Asthma or allergic disease (pleiotropy)3.000000e-10
GCST009856_12Leukocyte telomere length6.000000e-14
GCST010002_71Refractive error1.000000e-14
GCST90002390_678Mean corpuscular hemoglobin1.000000e-15

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004527mean corpuscular hemoglobin

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, increases methylation4
sodium arsenitedecreases expression, increases expression3
Tobacco Smoke Pollutiondecreases expression2
Cyclosporinedecreases expression2
Particulate Matterincreases abundance, affects cotreatment, decreases expression2
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aaffects expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
butyraldehydeincreases expression1
tobacco tardecreases expression1
pentanalincreases expression1
CGP 52608affects binding, increases reaction1
jinfukangincreases expression, affects cotreatment1
NSC 689534decreases expression, affects binding1
Temozolomideincreases expression1
Sunitinibdecreases expression1
Acetaminophenaffects expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects methylation1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation, decreases methylation1
Cisplatinincreases expression, affects cotreatment1
Copperdecreases expression, affects binding1
Cyclophosphamideincreases expression1
Dactinomycinincreases expression1
Doxorubicindecreases expression1
Estradioldecreases expression, affects cotreatment1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Glucosedecreases expression1
Methyl Methanesulfonateincreases expression1

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.