SPIN4

gene
On this page

Also known as FLJ44984TDRD28

Summary

SPIN4 (spindlin family member 4, HGNC:27040) is a protein-coding gene on chromosome Xq11.1, encoding Spindlin-4 (Q56A73). Binds to acetylated and methylated histones, including H3K4me3 and H4K20me3, probably acting as a histone reader that recognizes chromatin marks and mediates downstream cellular effects.

Enables methylated histone binding activity. Involved in negative regulation of cell population proliferation and positive regulation of canonical Wnt signaling pathway. Located in chromatin; cytoplasm; and nucleus.

Source: NCBI Gene 139886 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Lui-Jee-Baron syndrome (Moderate, GenCC)
  • Clinical variants (ClinVar): 12 total — 1 pathogenic
  • Phenotypes (HPO): 15
  • Druggable target: yes
  • MANE Select transcript: NM_001012968

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:27040
Approved symbolSPIN4
Namespindlin family member 4
LocationXq11.1
Locus typegene with protein product
StatusApproved
AliasesFLJ44984, TDRD28
Ensembl geneENSG00000186767
Ensembl biotypeprotein_coding
OMIM301113
Entrez139886

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000374884

RefSeq mRNA: 1 — MANE Select: NM_001012968 NM_001012968

CCDS: CCDS43964

Canonical transcript exons

ENST00000374884 — 1 exons

ExonStartEnd
ENSE000014650156334722863351332

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 96.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.8884 / max 209.7798, expressed in 1638 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
19944212.94141586
1994431.1905698
1994410.3709206
1994400.3304177
1994390.055215

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011596.59silver quality
esophagus squamous epitheliumUBERON:000692092.53gold quality
epithelial cell of pancreasCL:000008388.74silver quality
epithelium of nasopharynxUBERON:000195187.64gold quality
visceral pleuraUBERON:000240187.58gold quality
gingival epitheliumUBERON:000194987.42gold quality
gingivaUBERON:000182885.68gold quality
oral cavityUBERON:000016785.44gold quality
trabecular bone tissueUBERON:000248384.83gold quality
oviduct epitheliumUBERON:000480484.58gold quality
germinal epithelium of ovaryUBERON:000130484.17gold quality
epithelium of mammary glandUBERON:000324483.98gold quality
mammary ductUBERON:000176583.93gold quality
ventricular zoneUBERON:000305382.88gold quality
parietal pleuraUBERON:000240082.70gold quality
ganglionic eminenceUBERON:000402382.50gold quality
mucosa of sigmoid colonUBERON:000499382.18gold quality
bone marrowUBERON:000237181.09gold quality
lower lobe of lungUBERON:000894980.78gold quality
colonic mucosaUBERON:000031780.71gold quality
tibiaUBERON:000097980.51gold quality
palpebral conjunctivaUBERON:000181279.95gold quality
endometriumUBERON:000129579.37gold quality
Brodmann (1909) area 23UBERON:001355478.42gold quality
amniotic fluidUBERON:000017378.30gold quality
ileal mucosaUBERON:000033178.14gold quality
placentaUBERON:000198778.09gold quality
mammary glandUBERON:000191178.05gold quality
thoracic mammary glandUBERON:000520078.00gold quality
mucosa of paranasal sinusUBERON:000503077.95gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

137 targeting SPIN4, 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-3163100.0077.238605
HSA-MIR-5692A100.0074.406850
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-340-5P100.0072.504437
HSA-MIR-656-3P100.0072.152788
HSA-MIR-4533100.0069.482758
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-428299.9975.366408
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-366299.9973.825684
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-477599.9875.006394
HSA-MIR-1213699.9872.815713
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-314899.9775.066478
HSA-MIR-548AN99.9770.912817
HSA-MIR-590-3P99.9674.346478
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-211099.9666.681930

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriospinbENSDARG00000035697
danio_reriospinaENSDARG00000058949
mus_musculusSpin4ENSMUSG00000071722
rattus_norvegicusSpin4ENSRNOG00000077287

Paralogs (4): SPIN1 (ENSG00000106723), SPIN2A (ENSG00000147059), SPIN2B (ENSG00000186787), SPIN3 (ENSG00000204271)

Protein

Protein identifiers

Spindlin-4Q56A73 (reviewed: Q56A73)

All UniProt accessions (1): Q56A73

UniProt curated annotations — full annotation on UniProt →

Function. Binds to acetylated and methylated histones, including H3K4me3 and H4K20me3, probably acting as a histone reader that recognizes chromatin marks and mediates downstream cellular effects. Promotes canonical WNT signaling, and is involved in the down-regulation of cell proliferation.

Subunit / interactions. Interacts with C11orf84/SPINDOC. Associates with chromatin.

Subcellular location. Cytoplasm. Nucleus.

Disease relevance. Lui-Jee-Baron syndrome (LJBS) [MIM:301114] An X-linked disorder characterized by prenatal onset, generalized overgrowth, extreme tall stature, enlarged liver and spleen, macrocephaly, dysmorphic features, and normal development. Hemizygous males are more severely affected than heterozygous females. The disease may be caused by variants affecting the gene represented in this entry. A variant causing frameshift and truncation of the SPIN4 protein has been found in one family with Lui-Jee-Baron syndrome. In mice, SPIN4 truncating mutations result in features recapitulating the human disease, including generalized overgrowth and increased longitudinal bone growth. Growth plate analysis of mutant mice reveales increased cell proliferation in the proliferative zone and an increased number of progenitor chondrocytes in the resting zone.

Similarity. Belongs to the SPIN/STSY family.

RefSeq proteins (1): NP_001012986* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003671SPIN/SstyFamily
IPR042567SPIN/Ssty_sfHomologous_superfamily

Pfam: PF02513

UniProt features (29 total): strand 16, region of interest 5, turn 2, helix 2, site 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
4UY4X-RAY DIFFRACTION1.86
9T31X-RAY DIFFRACTION2.04

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q56A73-F182.170.64

Functional residue map

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

Catalytic / active sites (2): 159 (histone h3k4me3 and h3r8me2a binding); 170 (histone h3k4me3 and h3r8me2a binding)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 152 (showing top): GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_CANONICAL_WNT_SIGNALING_PATHWAY, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, GOBP_POSITIVE_REGULATION_OF_WNT_SIGNALING_PATHWAY, GRADE_COLON_AND_RECTAL_CANCER_DN, VERNELL_RETINOBLASTOMA_PATHWAY_UP, KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3, GEORGES_TARGETS_OF_MIR192_AND_MIR215, VECCHI_GASTRIC_CANCER_EARLY_UP, WHITFIELD_CELL_CYCLE_G1_S, CHICAS_RB1_TARGETS_SENESCENT, CHICAS_RB1_TARGETS_GROWING, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN, chrXq11

GO Biological Process (5): regulation of DNA-templated transcription (GO:0006355), gamete generation (GO:0007276), negative regulation of cell population proliferation (GO:0008285), positive regulation of canonical Wnt signaling pathway (GO:0090263), chromatin organization (GO:0006325)

GO Molecular Function (2): histone H3K4me3 reader activity (GO:0140002), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
sexual reproduction1
multicellular organismal reproductive process1
cell population proliferation1
regulation of cell population proliferation1
negative regulation of cellular process1
positive regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
regulation of canonical Wnt signaling pathway1
cellular component organization1
histone H3 reader activity1
binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

288 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SPIN4ARHGEF9O43307512
SPIN4GMCL1Q96IK5506
SPIN4HP1BP3Q5SSJ5466
SPIN4ATOSBQ7L5A3438
SPIN4TAF13Q15543435
SPIN4SPINDOCQ9BUA3400
SPIN4C2CD5Q86YS7385
SPIN4MAGEA10P43363383
SPIN4CAPN6Q9Y6Q1382
SPIN4ALG13Q9NP73379
SPIN4C10orf71Q711Q0377
SPIN4HEPHQ9BQS7372
SPIN4EDA2RQ9HAV5372
SPIN4KCTD3Q9Y597364
SPIN4ADAM20O43506360

IntAct

12 interactions, top by confidence:

ABTypeScore
SPIN1PAX3psi-mi:“MI:0914”(association)0.530
SPIN4PRMT6psi-mi:“MI:0914”(association)0.530
Mpsi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
ATG16L1psi-mi:“MI:0914”(association)0.350
SPIN4FBXO11psi-mi:“MI:0914”(association)0.350
PRTN3GOLIM4psi-mi:“MI:0914”(association)0.350
SPIN4MBL2psi-mi:“MI:0914”(association)0.350
SPIN4DIS3L2psi-mi:“MI:0914”(association)0.350

BioGRID (20): SPIN4 (Affinity Capture-RNA), SPIN4 (Affinity Capture-RNA), SPIN4 (Affinity Capture-MS), SPIN4 (Affinity Capture-MS), SPIN4 (Affinity Capture-MS), SPIN4 (Affinity Capture-MS), DCAF16 (Affinity Capture-MS), PRMT6 (Affinity Capture-MS), PKLR (Affinity Capture-MS), TPK1 (Affinity Capture-MS), MBL2 (Affinity Capture-MS), SPIN1 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), DCAF16 (Affinity Capture-Western), SPIN4 (Affinity Capture-Western)

ESM2 similar proteins: B3H754, C6KIE6, F4I8W1, F4ISV9, F4J4N3, F4K3G5, F4K487, K7TQE3, O22267, O23610, O80568, P13675, P59178, Q0WS06, Q32N90, Q500V5, Q56A73, Q683D5, Q6AUQ7, Q6DBH0, Q6NKN8, Q84WJ0, Q8K1L2, Q8RXM6, Q94HV8, Q969R5, Q9C5P0, Q9C5Q9, Q9C7I9, Q9C8N7, Q9C8N9, Q9FFA0, Q9FGS8, Q9FJX8, Q9FJX9, Q9FMV0, Q9FT92, Q9FV02, Q9FX25, Q9LG02

Diamond homologs: P13675, Q2KI39, Q4V8J7, Q56A73, Q5JUX0, Q5R997, Q5RA80, Q5RAW7, Q61142, Q6NVE3, Q8K1L2, Q90WG1, Q90WG2, Q99865, Q9BPZ2, Q9Y657

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance11
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2671851NM_001012968.3(SPIN4):c.312_313del (p.Arg104fs)Pathogenic

SpliceAI

88 predictions. Top by Δscore:

VariantEffectΔscore
X:63351164:G:Cdonor_gain0.9900
X:63351163:A:ACdonor_gain0.9800
X:63351163:AG:Adonor_gain0.9600
X:63350144:TCGCC:Tdonor_gain0.9500
X:63350124:A:ACdonor_gain0.9000
X:63350180:TGG:Tdonor_gain0.8600
X:63350125:A:Cdonor_gain0.8300
X:63350805:G:Tacceptor_gain0.8300
X:63348491:C:Gacceptor_gain0.8100
X:63350143:TTCGC:Tdonor_gain0.7500
X:63350150:C:CTdonor_gain0.7400
X:63350204:C:CTdonor_gain0.7200
X:63350205:C:CTdonor_gain0.7000
X:63350203:TC:Tdonor_gain0.6900
X:63350147:C:CTdonor_gain0.6800
X:63351164:G:Adonor_gain0.6400
X:63350178:CTTGG:Cdonor_gain0.6200
X:63350729:T:TAacceptor_gain0.5800
X:63351157:C:CTdonor_gain0.5800
X:63348492:T:TGacceptor_gain0.5200
X:63350151:C:CTdonor_gain0.5100
X:63351158:C:CTdonor_gain0.5000
X:63350807:T:TCacceptor_gain0.4700
X:63350788:ACCCC:Aacceptor_gain0.4400
X:63350789:CCCCC:Cacceptor_gain0.4400
X:63351159:A:ACdonor_gain0.4400
X:63351160:C:CCdonor_gain0.4400
X:63350804:CGGT:Cacceptor_gain0.4300
X:63351160:CTTAG:Cdonor_gain0.4300
X:63350994:CTA:Cdonor_gain0.4100

AlphaMissense

1633 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:63350439:A:CF127L0.999
X:63350439:A:TF127L0.999
X:63350441:A:GF127L0.999
X:63350118:A:CF234L0.998
X:63350118:A:TF234L0.998
X:63350120:A:GF234L0.998
X:63350293:A:GL176S0.998
X:63350364:A:CF152L0.998
X:63350364:A:TF152L0.998
X:63350366:A:GF152L0.998
X:63350673:C:AW49C0.997
X:63350673:C:GW49C0.997
X:63350440:A:CF127C0.996
X:63350588:A:GY78H0.996
X:63350589:T:AK77N0.996
X:63350589:T:GK77N0.996
X:63350639:C:GG61R0.996
X:63350119:A:GF234S0.995
X:63350311:T:AD170V0.995
X:63350335:A:TL162H0.995
X:63350354:A:GY156H0.995
X:63350398:A:TV141D0.995
X:63350405:C:GG139R0.995
X:63350440:A:GF127S0.995
X:63350591:T:CK77E0.995
X:63350629:A:TL64H0.995
X:63350686:A:CI45S0.995
X:63350686:A:GI45T0.995
X:63350686:A:TI45N0.995
X:63350121:C:AK233N0.994

dbSNP variants (sampled 300 via entrez): RS1053713 (X:63347590 T>C), RS111287985 (X:63347451 T>C), RS111923761 (X:63348588 G>T), RS113579085 (X:63352061 A>G), RS1156493888 (X:63352627 G>A,T), RS1156688942 (X:63351563 C>T), RS1158595894 (X:63348004 C>G,T), RS1158691165 (X:63347395 T>C), RS1159270746 (X:63353257 G>T), RS1159434178 (X:63346735 C>T), RS1159506306 (X:63352037 T>A,C), RS1159634932 (X:63349401 TAAA>T,TA,TAA), RS1159704013 (X:63351198 G>A), RS1160115370 (X:63351580 G>C,T), RS1160307389 (X:63350220 G>A)

Disease associations

OMIM: gene MIM:301113 | disease phenotypes: MIM:301114

GenCC curated gene-disease

DiseaseClassificationInheritance
Lui-Jee-Baron syndromeModerateX-linked

Mondo (1): Lui-Jee-Baron syndrome (MONDO:0957919)

Orphanet (0):

HPO phenotypes

15 total (15 of 15 shown, HPO-id order):

HPOTerm
HP:0000256Macrocephaly
HP:0000411Protruding ear
HP:0000490Deeply set eye
HP:0000494Downslanted palpebral fissures
HP:0001249Intellectual disability
HP:0001417X-linked inheritance
HP:0001520Large for gestational age
HP:0001548Overgrowth
HP:0001744Splenomegaly
HP:0001763Pes planus
HP:0002002Deep philtrum
HP:0002240Hepatomegaly
HP:0002343Normal pressure hydrocephalus
HP:0003577Congenital onset
HP:0006610Wide intermamillary distance

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4523321 (SINGLE PROTEIN)

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

ChEMBL bioactivities

3 potent at pChembl≥5 of 3 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.74Kd18.1nMCHEMBL4451634
6.77Kd170nMCHEMBL4552020
6.15Kd710nMCHEMBL5594627

PubChem BioAssay actives

3 with measured affinity, of 5 total; 3 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
2-[4-[2-[[2-[3-[2-amino-5-(cyclopropylmethoxy)-3,3-dimethylindol-6-yl]oxypropyl]-1,3-dihydroisoindol-5-yl]oxy]ethyl]triazol-1-yl]-1-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]ethanone1526487: Binding affinity to recombinant human His-tagged SPIN4 (36 to 249 residues) expressed in Escherichia coli BL21 (DE3) assessed as dissociation constant by isothermal titration calorimetrykd0.0181uM
[3-(aminomethyl)-5-[3-(1,3-dihydroisoindol-2-yl)propoxy]-4-methoxyphenyl]methanamine1578937: Inhibition of recombinant human N-terminal His6-tagged SPIN4 (36 to 249 residues) expressed in Escherichia coli BL21 (DE3) cells assessed as dissociation constant by isothermal titration calorimetrykd0.1700uM
N-[7-[3-(1,3-dihydroisoindol-2-yl)propoxy]-6-methoxy-4-pyrrolidin-1-ylquinazolin-2-yl]-N’,N’-dimethylethane-1,2-diamine2103453: Binding affinity to human N-terminal His6 tagged SPIN4 (T36 to P249 residues) expressed in Escherichia coli BL21 (DE3) assessed as dissociation constant by isothermal titration calorimetrykd0.7100uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression5
Valproic Acidaffects expression, decreases expression, increases expression4
bisphenol Aaffects expression, decreases expression2
trichostatin Aaffects cotreatment, increases expression2
Benzo(a)pyreneaffects methylation, increases expression, increases methylation2
Endosulfandecreases expression2
Cyclosporinedecreases expression2
triphenyl phosphateaffects expression1
testosterone undecanoateaffects cotreatment, decreases expression1
mono-(2-ethylhexyl)phthalateincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chloridedecreases expression1
butyraldehydedecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
potassium chromate(VI)decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
resorcinolincreases expression1
beta-methylcholineaffects expression1
pentanaldecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
abrinedecreases expression1
dorsomorphinincreases expression, affects cotreatment1
NSC 689534affects binding, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Air Pollutantsincreases abundance, decreases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1

ChEMBL screening assays

4 unique, capped per target: 4 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4323087BindingBinding affinity to recombinant human His-tagged SPIN4 (36 to 249 residues) expressed in Escherichia coli BL21 (DE3) assessed as melting temperature at 20 uM by Sypro orange dye based differential scanning fluorimetryA Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function. — J Med Chem

Clinical trials (associated diseases)

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

  • Associated diseases: Lui-Jee-Baron syndrome
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Lui-Jee-Baron syndrome