STMN4

Summary

STMN4 (stathmin 4, HGNC:16078) is a protein-coding gene on chromosome 8p21.2, encoding Stathmin-4 (Q9H169). Exhibits microtubule-destabilizing activity.

Predicted to enable tubulin binding activity. Predicted to be involved in microtubule depolymerization; neuron projection development; and regulation of microtubule polymerization or depolymerization. Predicted to be located in Golgi apparatus and growth cone. Predicted to be active in cytoplasm and neuron projection.

Source: NCBI Gene 81551 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_030795

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16078
Approved symbol	STMN4
Name	stathmin 4
Location	8p21.2
Locus type	gene with protein product
Status	Approved
Aliases	RB3
Ensembl gene	ENSG00000015592
Ensembl biotype	protein_coding
OMIM	620740
Entrez	81551

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 retained_intron

ENST00000265770, ENST00000350889, ENST00000519614, ENST00000519997, ENST00000522750, ENST00000522908, ENST00000523048, ENST00000908225, ENST00000908226, ENST00000955363, ENST00000955364

RefSeq mRNA: 10 — MANE Select: NM_030795 NM_001283053, NM_001283054, NM_001283055, NM_001394383, NM_001394384, NM_001394385, NM_001394386, NM_001394387, NM_001394388, NM_030795

CCDS: CCDS6055, CCDS64851, CCDS64852, CCDS64854

Canonical transcript exons

ENST00000350889 — 7 exons

Exon	Start	End
ENSE00001041541	27239971	27240162
ENSE00001041546	27241054	27241262
ENSE00001899075	27235308	27236905
ENSE00002129297	27258351	27258404
ENSE00003512503	27241677	27241757
ENSE00003603937	27242397	27242492
ENSE00003666498	27243711	27243801

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 99.31.

FANTOM5 (CAGE): breadth broad, TPM avg 8.2625 / max 803.8024, expressed in 250 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
92438	7.5861	240
92439	0.6763	129

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	99.31	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	99.20	gold quality
spinal cord	UBERON:0002240	98.89	gold quality
ganglionic eminence	UBERON:0004023	98.69	gold quality
prefrontal cortex	UBERON:0000451	98.60	gold quality
middle temporal gyrus	UBERON:0002771	98.45	gold quality
right frontal lobe	UBERON:0002810	98.31	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.25	gold quality
frontal cortex	UBERON:0001870	98.11	gold quality
frontal lobe	UBERON:0016525	98.11	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.08	gold quality
hypothalamus	UBERON:0001898	98.05	gold quality
neocortex	UBERON:0001950	98.04	gold quality
ventricular zone	UBERON:0003053	98.00	gold quality
amygdala	UBERON:0001876	97.92	gold quality
cerebral cortex	UBERON:0000956	97.86	gold quality
primary visual cortex	UBERON:0002436	97.84	gold quality
Ammon’s horn	UBERON:0001954	97.75	gold quality
cingulate cortex	UBERON:0003027	97.73	gold quality
anterior cingulate cortex	UBERON:0009835	97.73	gold quality
medial globus pallidus	UBERON:0002477	97.69	gold quality
globus pallidus	UBERON:0001875	97.58	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.50	gold quality
Brodmann (1909) area 46	UBERON:0006483	97.50	gold quality
occipital lobe	UBERON:0002021	97.45	gold quality
inferior vagus X ganglion	UBERON:0005363	97.42	gold quality
telencephalon	UBERON:0001893	97.41	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.35	gold quality
cerebellar cortex	UBERON:0002129	97.30	gold quality
cerebellar hemisphere	UBERON:0002245	97.29	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-11121	yes	2539.51
E-MTAB-6911	yes	451.51
E-HCAD-5	yes	54.08
E-MTAB-7316	yes	13.60
E-GEOD-93593	yes	10.69
E-HCAD-10	yes	5.18
E-MTAB-8894	no	1623.43
E-MTAB-9154	no	1392.59
E-MTAB-7303	no	367.34
E-ANND-3	no	2.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting STMN4, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-1197	99.70	67.75	1027
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-3682-3P	99.58	67.63	865
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-6828-5P	99.31	69.21	1433
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-4727-5P	99.23	67.55	1154
HSA-MIR-122B-3P	99.21	68.90	1333
HSA-MIR-21-3P	99.21	68.95	1312
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-10524-5P	99.05	66.08	963
HSA-MIR-1909-3P	99.03	66.56	1662

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	stmn4l	ENSDARG00000043932
mus_musculus	Stmn4	ENSMUSG00000022044
rattus_norvegicus	Stmn4	ENSRNOG00000053334
drosophila_melanogaster	stai	FBGN0266521

Paralogs (4): STMN2 (ENSG00000104435), STMN1 (ENSG00000117632), STMN3 (ENSG00000197457), STMND1 (ENSG00000230873)

Protein

Protein identifiers

Stathmin-4 — Q9H169 (reviewed: Q9H169)

Alternative names: Stathmin-like protein B3

All UniProt accessions (3): Q9H169, E5RIR6, E7EVN3

UniProt curated annotations — full annotation on UniProt →

Function. Exhibits microtubule-destabilizing activity.

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

Similarity. Belongs to the stathmin family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9H169-1	1	yes
Q9H169-2	2
Q9H169-3	3
Q9H169-4	4

RefSeq proteins (10): NP_001269982, NP_001269983, NP_001269984, NP_001381312, NP_001381313, NP_001381314, NP_001381315, NP_001381316, NP_001381317, NP_110422* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000956	Stathmin_fam	Family
IPR030514	Stathmin_CS	Conserved_site
IPR036002	Stathmin_sf	Homologous_superfamily

Pfam: PF00836

UniProt features (15 total): splice variant 3, strand 2, helix 2, lipid moiety-binding region 2, chain 1, domain 1, sequence conflict 1, region of interest 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

10 structures.

PDB	Method	Resolution (Å)
9F07	X-RAY DIFFRACTION	2.21
6O5M	X-RAY DIFFRACTION	2.3
6BR1	X-RAY DIFFRACTION	2.3
6NNG	X-RAY DIFFRACTION	2.4
6BRF	X-RAY DIFFRACTION	2.5
7CPD	X-RAY DIFFRACTION	2.51
6O61	X-RAY DIFFRACTION	2.6
6PC4	X-RAY DIFFRACTION	2.6
6BRY	X-RAY DIFFRACTION	2.7
6O5N	X-RAY DIFFRACTION	3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H169-F1	84.52	0.58

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 (3): 90, 20, 22

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 130 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GNF2_RTN1, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, AAGCCAT_MIR135A_MIR135B, GOBP_NEUROGENESIS, GGGTGGRR_PAX4_03, EFC_Q6, CDP_01, chr8p21, GOBP_MICROTUBULE_DEPOLYMERIZATION, NF1_Q6_01, TGCTGAY_UNKNOWN, TGACATY_UNKNOWN, AACTTT_UNKNOWN, GOBP_PROTEIN_DEPOLYMERIZATION

GO Biological Process (3): microtubule depolymerization (GO:0007019), regulation of microtubule polymerization or depolymerization (GO:0031110), neuron projection development (GO:0031175)

GO Molecular Function (2): tubulin binding (GO:0015631), protein binding (GO:0005515)

GO Cellular Component (6): cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), 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:

Category	Terms
microtubule polymerization or depolymerization	2
cellular anatomical structure	2
protein depolymerization	1
supramolecular fiber organization	1
regulation of microtubule cytoskeleton organization	1
neuron development	1
plasma membrane bounded cell projection organization	1
cytoskeletal protein binding	1
binding	1
intracellular anatomical structure	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
site of polarized growth	1
distal axon	1
plasma membrane bounded cell projection	1
neuron projection	1

Protein interactions and networks

STRING

1860 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STMN4	TTL	Q8NG68	577
STMN4	TUBA1B	P04687	541
STMN4	GNG3	P29798	490
STMN4	FHIP2B	Q86V87	459
STMN4	ACSBG1	Q96GR2	436
STMN4	SLC32A1	Q9H598	395
STMN4	SNRPN	P14648	369
STMN4	SLC1A2	P43004	363
STMN4	ABLIM2	Q6H8Q1	348
STMN4	RGSL1	A5PLK6	340
STMN4	TBCA	O75347	327
STMN4	SAXO1	Q8IYX7	302
STMN4	TUBD1	Q9UJT1	289
STMN4	KIF9	Q9HAQ2	288
STMN4	UBE3A	P78355	285
STMN4	CDK5RAP3	Q96JB5	285

IntAct

8 interactions, top by confidence:

A	B	Type	Score
STMN4	ANKRD13A	psi-mi:“MI:0915”(physical association)	0.400
STMN4	MTNR1B	psi-mi:“MI:0915”(physical association)	0.370
STMN4	NUFIP2	psi-mi:“MI:0915”(physical association)	0.370
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
STMN4	TRAPPC3	psi-mi:“MI:0914”(association)	0.350
STMN4	IMMT	psi-mi:“MI:0915”(physical association)	0.000
STMN4	PHIP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (51): C7orf43 (Affinity Capture-MS), TRAPPC9 (Affinity Capture-MS), TRAPPC6B (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), STMN4 (Affinity Capture-MS), TRAPPC4 (Affinity Capture-MS), VTA1 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS), TRAPPC3 (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), PTPRD (Affinity Capture-MS), GCA (Affinity Capture-MS), STMN4 (Two-hybrid), STMN4 (Affinity Capture-Western)

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

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	1
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

852 predictions. Top by Δscore:

Variant	Effect	Δscore
8:27236901:TTGTC:T	acceptor_gain	1.0000
8:27236902:TGTC:T	acceptor_gain	1.0000
8:27236903:GTC:G	acceptor_gain	1.0000
8:27236904:TC:T	acceptor_gain	1.0000
8:27236905:CC:C	acceptor_gain	1.0000
8:27236906:C:CC	acceptor_gain	1.0000
8:27236906:CT:C	acceptor_loss	1.0000
8:27239965:CCTCA:C	donor_loss	1.0000
8:27239966:CTCA:C	donor_loss	1.0000
8:27239967:TCA:T	donor_loss	1.0000
8:27239968:CA:C	donor_loss	1.0000
8:27239969:ACCT:A	donor_loss	1.0000
8:27239970:CCTT:C	donor_gain	1.0000
8:27240012:C:A	donor_gain	1.0000
8:27240161:TA:T	acceptor_gain	1.0000
8:27240163:C:CC	acceptor_gain	1.0000
8:27240163:C:CG	acceptor_loss	1.0000
8:27240164:T:C	acceptor_loss	1.0000
8:27240172:C:CT	acceptor_gain	1.0000
8:27240173:A:AC	acceptor_gain	1.0000
8:27240173:A:C	acceptor_gain	1.0000
8:27241049:TTTAC:T	donor_loss	1.0000
8:27241050:TTAC:T	donor_loss	1.0000
8:27241051:TACCT:T	donor_loss	1.0000
8:27241052:A:AC	donor_gain	1.0000
8:27241052:ACC:A	donor_loss	1.0000
8:27241052:ACCTT:A	donor_gain	1.0000
8:27241053:C:CC	donor_gain	1.0000
8:27241053:CCTT:C	donor_gain	1.0000
8:27241053:CCTTC:C	donor_gain	1.0000

AlphaMissense

1433 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:27241180:A:C	F64L	0.999
8:27241180:A:T	F64L	0.999
8:27241182:A:G	F64L	0.999
8:27239981:A:G	L167P	0.998
8:27239997:C:G	A162P	0.998
8:27240009:C:G	A158P	0.998
8:27240060:C:G	A141P	0.998
8:27240122:C:G	R120P	0.998
8:27241057:C:A	R105S	0.998
8:27241057:C:G	R105S	0.998
8:27241061:C:G	R104P	0.998
8:27241071:C:G	A101P	0.998
8:27236883:C:G	R178P	0.997
8:27236896:C:G	A174P	0.997
8:27239984:C:G	R166P	0.997
8:27240000:C:G	A161P	0.997
8:27240002:A:G	L160P	0.997
8:27240013:C:A	R156S	0.997
8:27240013:C:G	R156S	0.997
8:27240047:A:G	L145P	0.997
8:27240093:C:G	A130P	0.997
8:27240143:A:G	L113P	0.997
8:27240153:C:G	A110P	0.997
8:27241070:G:T	A101D	0.997
8:27241074:C:G	A100P	0.997
8:27241079:A:G	L98P	0.997
8:27241169:A:G	L68P	0.997
8:27240134:A:G	L116P	0.996
8:27241058:C:G	R105T	0.996
8:27241175:A:T	V66D	0.996

dbSNP variants (sampled 300 via entrez): RS1000107120 (8:27252363 A>C,G), RS1000145256 (8:27238044 C>T), RS1000145487 (8:27259070 C>G), RS1000160648 (8:27245932 A>G), RS1000382245 (8:27240274 G>A), RS1000409934 (8:27250565 G>A), RS1000452933 (8:27239501 C>T), RS1000477859 (8:27251569 T>C), RS1000505085 (8:27235690 C>A,T), RS1000599610 (8:27235436 T>G), RS1000816636 (8:27240612 T>C), RS1000892163 (8:27246272 G>A), RS1000958623 (8:27251955 C>A), RS1000999853 (8:27256788 T>C), RS1001055044 (8:27241212 C>G,T)

Disease associations

OMIM: gene MIM:620740 | 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):

Study	Trait	p-value
GCST009377_2	Bone mineral density	2.000000e-07
GCST009378_11	Bone mineral content	7.000000e-07
GCST009378_7	Bone mineral content	6.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007620	volumetric bone mineral density
EFO:0007621	bone mineral content measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	4
Cadmium Chloride	decreases expression, increases expression	3
Benzo(a)pyrene	increases expression, increases methylation, affects methylation	2
methylmercuric chloride	decreases expression	1
arsenite	decreases methylation	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
butyraldehyde	increases expression	1
15-acetyldeoxynivalenol	increases expression	1
entinostat	decreases expression	1
abrine	increases expression	1
Decitabine	affects expression	1
Amphotericin B	increases expression	1
Cisplatin	affects expression	1
Cytarabine	increases response to substance	1
Diethylhexyl Phthalate	decreases expression	1
N-Nitrosopyrrolidine	increases expression	1
Niclosamide	increases expression	1
Aflatoxin B1	increases expression	1
Okadaic Acid	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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