STMND1

Summary

STMND1 (stathmin domain containing 1, HGNC:44668) is a protein-coding gene on chromosome 6p22.3, encoding Stathmin domain-containing protein 1 (H3BQB6).

Predicted to be involved in regulation of microtubule polymerization or depolymerization.

Source: NCBI Gene 401236 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 48 total
• MANE Select transcript: NM_001190766

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44668
Approved symbol	STMND1
Name	stathmin domain containing 1
Location	6p22.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23152
Ensembl gene	ENSG00000230873
Ensembl biotype	protein_coding
Entrez	401236

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000354384, ENST00000366215, ENST00000536551, ENST00000907738

RefSeq mRNA: 1 — MANE Select: NM_001190766 NM_001190766

CCDS: CCDS58997

Canonical transcript exons

ENST00000536551 — 5 exons

Exon	Start	End
ENSE00002266322	17129112	17129243
ENSE00002279270	17120607	17120758
ENSE00002284098	17114962	17115139
ENSE00002305699	17102050	17102338
ENSE00003517930	17130594	17131378

Expression profiles

Bgee: expression breadth broad, 75 present calls, max score 91.37.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0576 / max 14.8412, expressed in 30 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66120	0.0389	18
66119	0.0187	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	91.37	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.81	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.64	gold quality
gall bladder	UBERON:0002110	73.45	gold quality
fallopian tube	UBERON:0003889	72.65	gold quality
body of pancreas	UBERON:0001150	72.47	gold quality
testis	UBERON:0000473	69.15	gold quality
right testis	UBERON:0004534	68.35	gold quality
left testis	UBERON:0004533	68.25	gold quality
right lung	UBERON:0002167	66.23	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.97	gold quality
pancreas	UBERON:0001264	64.41	gold quality
mucosa of transverse colon	UBERON:0004991	62.92	gold quality
endometrium	UBERON:0001295	62.19	gold quality
rectum	UBERON:0001052	58.06	gold quality
transverse colon	UBERON:0001157	56.00	gold quality
lung	UBERON:0002048	55.54	gold quality
left uterine tube	UBERON:0001303	53.77	gold quality
stromal cell of endometrium	CL:0002255	51.71	silver quality
upper lobe of left lung	UBERON:0008952	51.36	gold quality
duodenum	UBERON:0002114	51.09	gold quality
pituitary gland	UBERON:0000007	50.23	gold quality
adenohypophysis	UBERON:0002196	50.09	gold quality
islet of Langerhans	UBERON:0000006	49.87	gold quality
colon	UBERON:0001155	48.83	gold quality
hypothalamus	UBERON:0001898	47.47	gold quality
colonic epithelium	UBERON:0000397	47.06	gold quality
endocervix	UBERON:0000458	46.65	gold quality
prefrontal cortex	UBERON:0000451	46.02	gold quality
superior frontal gyrus	UBERON:0002661	45.99	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting STMND1, 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-3646	100.00	73.56	5283
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-3160-5P	99.28	69.07	1938
HSA-MIR-1909-5P	98.94	64.01	484
HSA-MIR-5581-3P	98.55	70.31	1161
HSA-MIR-7843-3P	98.31	67.94	803
HSA-MIR-876-5P	97.99	68.49	1345

Literature-anchored findings (GeneRIF, showing 1)

• STMND1 is a phylogenetically ancient stathmin which localizes to motile cilia and exhibits nuclear translocation that is inhibited when soluble tubulin concentration increases. (PMID:38630521)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	stmnd1	ENSDARG00000102611
mus_musculus	Stmnd1	ENSMUSG00000063529
rattus_norvegicus	Stmnd1	ENSRNOG00000031595
drosophila_melanogaster	stai	FBGN0266521

Paralogs (4): STMN4 (ENSG00000015592), STMN2 (ENSG00000104435), STMN1 (ENSG00000117632), STMN3 (ENSG00000197457)

Protein

Protein identifiers

Stathmin domain-containing protein 1 — H3BQB6 (reviewed: H3BQB6)

All UniProt accessions (2): H3BQB6, H3BMF7

RefSeq proteins (1): NP_001177695* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000956	Stathmin_fam	Family
IPR036002	Stathmin_sf	Homologous_superfamily

Pfam: PF00836

UniProt features (9 total): region of interest 3, compositionally biased region 2, initiator methionine 1, chain 1, domain 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H3BQB6-F1	63.83	0.15

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): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_NEUROGENESIS, GOBP_MICROTUBULE_DEPOLYMERIZATION, GOBP_PROTEIN_DEPOLYMERIZATION, GOCC_NEURON_PROJECTION, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_REGULATION_OF_MICROTUBULE_POLYMERIZATION_OR_DEPOLYMERIZATION, GOBP_REGULATION_OF_CYTOSKELETON_ORGANIZATION, GOMF_CYTOSKELETAL_PROTEIN_BINDING, GOBP_MICROTUBULE_CYTOSKELETON_ORGANIZATION, GOBP_PROTEIN_CONTAINING_COMPLEX_DISASSEMBLY, LEE_BMP2_TARGETS_UP, GOBP_SUPRAMOLECULAR_FIBER_ORGANIZATION, CBX7_TARGET_GENES, RYBP_TARGET_GENES

GO Biological Process (1): regulation of microtubule polymerization or depolymerization (GO:0031110)

GO Molecular Function (0):

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule polymerization or depolymerization	1
regulation of microtubule cytoskeleton organization	1

Protein interactions and networks

STRING

146 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STMND1	KIF13A	Q9H1H9	646
STMND1	ATXN1	P54253	595
STMND1	RBM24	Q9BX46	570
STMND1	SMOC2	Q9H3U7	512
STMND1	FAM8A1	Q9UBU6	474
STMND1	MYLIP	Q8WY64	473
STMND1	ATXN1L	P0C7T5	458
STMND1	SYNDIG1L	A6NDD5	447
STMND1	MRGPRE	Q86SM8	418
STMND1	TBC1D16	Q8TBP0	396
STMND1	NHLRC1	Q6VVB1	381
STMND1	TBC1D17	Q9HA65	370
STMND1	GMPR	P36959	366
STMND1	MAP3K6	O95382	305
STMND1	JARID2	Q92833	295

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A2CE83, A5D8S8, A5WUN7, D4AEC2, H3BQB6, O35867, O75167, O94885, P28290, P59808, P62025, Q08AD1, Q28GJ0, Q2MJV9, Q3KQW7, Q3KR53, Q3MHH7, Q3TRR0, Q3UH68, Q4KM62, Q4R6Q9, Q4R707, Q52KF3, Q5NVK0, Q5RC32, Q5RHU7, Q5TID7, Q63HQ0, Q69ZW3, Q6AYN9, Q6GLU8, Q6IRN6, Q6P3A1, Q6RFY2, Q7ZX27, Q80ZU5, Q86VQ0, Q8BYK5, Q8C1B1, Q8HYW0

Diamond homologs: H3BQB6, Q6P3A1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	42
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1092 predictions. Top by Δscore:

Variant	Effect	Δscore
6:17102336:AAG:A	donor_loss	1.0000
6:17102337:AGGT:A	donor_loss	1.0000
6:17102339:G:GA	donor_loss	1.0000
6:17114957:CACA:C	acceptor_loss	1.0000
6:17114958:A:AG	acceptor_gain	1.0000
6:17114958:ACAG:A	acceptor_gain	1.0000
6:17114959:C:G	acceptor_gain	1.0000
6:17114959:CA:C	acceptor_loss	1.0000
6:17114960:A:AC	acceptor_loss	1.0000
6:17114960:A:AG	acceptor_gain	1.0000
6:17114960:AG:A	acceptor_gain	1.0000
6:17114960:AGGCT:A	acceptor_gain	1.0000
6:17114961:G:GG	acceptor_gain	1.0000
6:17114961:GG:G	acceptor_gain	1.0000
6:17114961:GGC:G	acceptor_gain	1.0000
6:17114961:GGCT:G	acceptor_gain	1.0000
6:17114961:GGCTG:G	acceptor_gain	1.0000
6:17115125:GACGA:G	donor_gain	1.0000
6:17115136:TCAG:T	donor_loss	1.0000
6:17115137:CAG:C	donor_loss	1.0000
6:17115138:AG:A	donor_loss	1.0000
6:17115139:GG:G	donor_loss	1.0000
6:17115140:GT:G	donor_loss	1.0000
6:17115141:T:A	donor_loss	1.0000
6:17120601:T:TA	acceptor_gain	1.0000
6:17120602:G:A	acceptor_gain	1.0000
6:17120703:G:GT	donor_gain	1.0000
6:17129110:A:AG	acceptor_gain	1.0000
6:17129111:G:GA	acceptor_gain	1.0000
6:17129111:GTT:G	acceptor_gain	1.0000

AlphaMissense

1800 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:17120691:T:C	L115P	0.989
6:17120706:T:C	I120T	0.969
6:17120691:T:A	L115Q	0.968
6:17120703:G:T	G119V	0.963
6:17120679:T:C	I111T	0.958
6:17120679:T:G	I111S	0.957
6:17120706:T:G	I120S	0.957
6:17120709:T:A	I121K	0.949
6:17120702:G:A	G119R	0.937
6:17120702:G:C	G119R	0.937
6:17120709:T:C	I121T	0.933
6:17120691:T:G	L115R	0.927
6:17120679:T:A	I111N	0.907
6:17120709:T:G	I121R	0.905
6:17129155:T:C	L152P	0.904
6:17120700:A:C	Q118P	0.886
6:17120703:G:C	G119A	0.886
6:17120703:G:A	G119E	0.885
6:17120682:T:C	L112P	0.875
6:17120706:T:A	I120N	0.870
6:17129153:A:C	R151S	0.868
6:17129153:A:T	R151S	0.868
6:17130840:T:C	S264P	0.860
6:17120688:A:T	E114V	0.857
6:17120701:A:C	Q118H	0.829
6:17120701:A:T	Q118H	0.829
6:17102261:G:C	G2R	0.820
6:17120685:A:T	E113V	0.820
6:17130857:C:A	N269K	0.808
6:17130857:C:G	N269K	0.808

dbSNP variants (sampled 300 via entrez): RS1000025158 (6:17110649 C>G,T), RS1000077463 (6:17110981 T>A,C), RS1000345103 (6:17104797 T>C), RS1000509181 (6:17102814 A>G), RS1000616400 (6:17110967 G>A,C), RS1000772351 (6:17100125 C>T), RS1000782052 (6:17100135 T>A,G), RS1000811678 (6:17103111 T>C), RS1000945720 (6:17129938 T>C), RS1000977998 (6:17116773 A>C,G), RS1000981451 (6:17122070 C>T), RS1001008189 (6:17115164 C>T), RS1001064316 (6:17109499 A>T), RS1001116496 (6:17130090 G>A), RS1001398962 (6:17130411 A>C)

Disease associations

OMIM: gene `` | 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
GCST005316_635	Intelligence (MTAG)	5.000000e-09
GCST005316_636	Intelligence (MTAG)	3.000000e-09
GCST007433_3	Fulminant type 1 diabetes	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases expression	1
Endosulfan	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tunicamycin	increases expression	1
Okadaic Acid	increases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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