SLAIN2

gene
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Also known as FLJ21611

Summary

SLAIN2 (SLAIN family member 2, HGNC:29282) is a protein-coding gene on chromosome 4p11, encoding SLAIN motif-containing protein 2 (Q9P270). Binds to the plus end of microtubules and regulates microtubule dynamics and microtubule organization.

Involved in cytoplasmic microtubule organization; microtubule nucleation; and positive regulation of microtubule polymerization. Located in centrosome; cytosol; and microtubule plus-end.

Source: NCBI Gene 57606 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 116 total
  • MANE Select transcript: NM_020846

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29282
Approved symbolSLAIN2
NameSLAIN family member 2
Location4p11
Locus typegene with protein product
StatusApproved
AliasesFLJ21611
Ensembl geneENSG00000109171
Ensembl biotypeprotein_coding
OMIM610492
Entrez57606

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000264313, ENST00000505131, ENST00000506375, ENST00000510595, ENST00000512093, ENST00000888698, ENST00000917426, ENST00000942829, ENST00000942830

RefSeq mRNA: 1 — MANE Select: NM_020846 NM_020846

CCDS: CCDS47051

Canonical transcript exons

ENST00000264313 — 8 exons

ExonStartEnd
ENSE000007142844838256848382927
ENSE000007142904842012548420443
ENSE000015045184837969048379848
ENSE000020727144842201148426201
ENSE000020734204837789648378060
ENSE000035620754838364748383784
ENSE000042836364834152948342128
ENSE000042836374836984948369997

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 97.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.1718 / max 163.6229, expressed in 1803 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
475679.70591787
475663.37351526
475650.5462283
475640.3411139
475700.205170

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibialis anteriorUBERON:000138597.99gold quality
left ventricle myocardiumUBERON:000656697.51gold quality
deltoidUBERON:000147697.25gold quality
spermCL:000001997.18gold quality
calcaneal tendonUBERON:000370197.05gold quality
epithelial cell of pancreasCL:000008396.95gold quality
cardiac muscle of right atriumUBERON:000337996.62gold quality
hindlimb stylopod muscleUBERON:000425296.60gold quality
oviduct epitheliumUBERON:000480496.00gold quality
muscle of legUBERON:000138395.98gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450295.92gold quality
skeletal muscle tissueUBERON:000113495.90gold quality
vastus lateralisUBERON:000137995.90gold quality
skeletal muscle organUBERON:001489295.88gold quality
gastrocnemiusUBERON:000138895.82gold quality
biceps brachiiUBERON:000150795.70gold quality
colonic epitheliumUBERON:000039795.65gold quality
cortical plateUBERON:000534395.58gold quality
muscle tissueUBERON:000238595.50gold quality
smooth muscle tissueUBERON:000113595.41gold quality
quadriceps femorisUBERON:000137795.16gold quality
tendonUBERON:000004395.14gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451195.11gold quality
ileal mucosaUBERON:000033194.73gold quality
popliteal arteryUBERON:000225094.70gold quality
tibial arteryUBERON:000761094.69gold quality
cauda epididymisUBERON:000436094.67gold quality
upper arm skinUBERON:000426394.45gold quality
myocardiumUBERON:000234994.37gold quality
stromal cell of endometriumCL:000225594.24gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

344 targeting SLAIN2, 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-6833-3P100.0070.633197
HSA-MIR-4262100.0073.263931
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-4768-5P100.0069.492861
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-8485100.0077.574731
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3134100.0066.43777
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-12118100.0065.881270
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954

Literature-anchored findings (GeneRIF, showing 2)

  • Results identify SLAIN2 as a key component of microtubule plus end interaction networks. (PMID:21646404)
  • catastrophe inhibition by SLAIN2 and CLASP1 supports mesenchymal cell shape in soft 3D matrices by enabling microtubules to perform a load-bearing function. (PMID:27939686)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioslain2ENSDARG00000032114
mus_musculusSlain2ENSMUSG00000036087
rattus_norvegicusSlain2ENSRNOG00000002271

Paralogs (1): SLAIN1 (ENSG00000139737)

Protein

Protein identifiers

SLAIN motif-containing protein 2Q9P270 (reviewed: Q9P270)

All UniProt accessions (5): Q9P270, A0A024R9T6, D6REM5, D6RIF6, H0Y9L2

UniProt curated annotations — full annotation on UniProt →

Function. Binds to the plus end of microtubules and regulates microtubule dynamics and microtubule organization. Promotes cytoplasmic microtubule nucleation and elongation. Required for normal structure of the microtubule cytoskeleton during interphase.

Subunit / interactions. Interacts with CLIP1, CLIP2, CKAP5, CLASP1, MAPRE1 and MAPRE3.

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Widely expressed with highest levels in adult liver, testis and ovary, and lowest levels in adult pancreas and spleen and in fetal brain.

Post-translational modifications. Is highly phosphorylated during mitosis, but not during interphase. The highly phosphorylated form does not localize at microtubule plus ends and does not interact with MAPRE1 or CKAP5.

Domain organisation. The N-terminus forms a two-stranded coiled coil.

Similarity. Belongs to the SLAIN motif-containing family.

RefSeq proteins (1): NP_065897* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026179SlainFamily

Pfam: PF15301

UniProt features (44 total): modified residue 24, compositionally biased region 9, region of interest 4, sequence conflict 2, chain 1, site 1, mutagenesis site 1, helix 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3RDVX-RAY DIFFRACTION1.75

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P270-F154.690.11

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 (1): 581 (important for interaction with clip1)

Post-translational modifications (24): 1, 43, 48, 63, 88, 134, 147, 160, 179, 247, 250, 251, 254, 315, 323, 377, 391, 413, 433, 456 …

Mutagenesis-validated functional residues (1):

PositionPhenotype
581abolishes interaction with clip1.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 239 (showing top): GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MICROTUBULE_NUCLEATION, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_MICROTUBULE_POLYMERIZATION_OR_DEPOLYMERIZATION, GOBP_REGULATION_OF_MICROTUBULE_POLYMERIZATION, GOCC_CENTROSOME, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, chr4p11, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY

GO Biological Process (4): microtubule nucleation (GO:0007020), positive regulation of microtubule polymerization (GO:0031116), cytoplasmic microtubule organization (GO:0031122), regulation of microtubule polymerization (GO:0031113)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): centrosome (GO:0005813), cytosol (GO:0005829), microtubule cytoskeleton (GO:0015630), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), microtubule plus-end (GO:0035371)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
microtubule polymerization3
microtubule cytoskeleton organization2
cellular anatomical structure2
positive regulation of microtubule polymerization or depolymerization1
regulation of microtubule polymerization1
positive regulation of protein polymerization1
positive regulation of supramolecular fiber organization1
supramolecular fiber organization1
regulation of microtubule polymerization or depolymerization1
regulation of protein polymerization1
regulation of supramolecular fiber organization1
binding1
centriole1
microtubule organizing center1
cytoplasm1
cytoskeleton1
intracellular anatomical structure1
intracellular membraneless organelle1
microtubule end1

Protein interactions and networks

STRING

1706 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLAIN2CKAP5Q14008608
SLAIN2CLASP1Q7Z460554
SLAIN2SLC10A4Q96EP9539
SLAIN2CLASP2O75122529
SLAIN2ZC3H18Q86VM9528
SLAIN2OCIAD1Q9NX40527
SLAIN2CLASRPQ8N2M8501
SLAIN2NFXL1Q6ZNB6496
SLAIN2METTL26Q96S19478
SLAIN2ARHGEF10LQ9HCE6474
SLAIN2FRYLO94915454
SLAIN2CLIP2Q9UDT6445
SLAIN2MAPRE3Q9UPY8443
SLAIN2AKAP1Q92667426
SLAIN2AFMIDQ63HM1423

IntAct

68 interactions, top by confidence:

ABTypeScore
CKAP5TACC1psi-mi:“MI:0914”(association)0.800
YWHAGBLTP3Bpsi-mi:“MI:0914”(association)0.640
SLAIN2YWHAHpsi-mi:“MI:0914”(association)0.640
SLAIN2CKAP5psi-mi:“MI:0915”(physical association)0.620
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
YWHAHBLTP3Bpsi-mi:“MI:0914”(association)0.570
YWHAQIGLC7psi-mi:“MI:0914”(association)0.530
GRB2SH3PXD2Bpsi-mi:“MI:0914”(association)0.530
TSKSRGPD8psi-mi:“MI:0914”(association)0.530
TACC3HSPA8psi-mi:“MI:0914”(association)0.530
PTPRDSLAIN2psi-mi:“MI:0407”(direct interaction)0.440
SLAIN2DAPK1psi-mi:“MI:0407”(direct interaction)0.440
SLAIN2psi-mi:“MI:0407”(direct interaction)0.440
OgnSLAIN2psi-mi:“MI:0407”(direct interaction)0.440
SLAIN2SRPK2psi-mi:“MI:0217”(phosphorylation reaction)0.440
SLAIN2SRPK1psi-mi:“MI:0217”(phosphorylation reaction)0.440
YWHAZSLAIN2psi-mi:“MI:0915”(physical association)0.400
TACC3DHRS2psi-mi:“MI:0914”(association)0.350
Ckap5CCHCR1psi-mi:“MI:0914”(association)0.350
CKAP5TACC3psi-mi:“MI:0914”(association)0.350
MAGEA10XPO1psi-mi:“MI:0914”(association)0.350
SLAIN2TACC2psi-mi:“MI:0914”(association)0.350
SLAIN2TARS3psi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
E7COPEpsi-mi:“MI:0914”(association)0.350
SNAP23psi-mi:“MI:0914”(association)0.350
TUBA1ACAPZBpsi-mi:“MI:0914”(association)0.350
TUBA1AKIF2Apsi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (161): SLAIN2 (Affinity Capture-MS), SLAIN2 (Proximity Label-MS), SLAIN2 (Proximity Label-MS), SLAIN2 (Proximity Label-MS), SLAIN2 (Proximity Label-MS), SLAIN2 (Proximity Label-MS), SLAIN2 (Affinity Capture-MS), SLAIN2 (Affinity Capture-MS), ADRBK1 (Affinity Capture-MS), JARID2 (Affinity Capture-MS), P4HA1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), TRIM27 (Affinity Capture-MS), FXR1 (Affinity Capture-MS), YBX3 (Affinity Capture-MS)

ESM2 similar proteins: A0A088MLT8, A0JNC2, A2AQ25, A6H7A8, B3KU38, B5DF41, E1BEQ5, E9PSK7, O15079, O60271, Q157S1, Q3MHV6, Q4VCS5, Q58A65, Q5F3B1, Q5R595, Q5T5P2, Q62739, Q68ED7, Q68FF7, Q7KW14, Q7PQ25, Q80TM6, Q80U23, Q86YP4, Q8CHY6, Q8CI08, Q8IY63, Q8ND83, Q8TEK3, Q8VHG2, Q8VHI6, Q8VHR5, Q8WXI9, Q920B0, Q921D9, Q96QF0, Q99LB0, Q9C0H9, Q9DCB4

Diamond homologs: A8E4V2, Q0VA20, Q3MHV6, Q5XG16, Q68FF7, Q7SXC6, Q8CI08, Q8ND83, Q9P270

SIGNOR signaling

1 interactions.

AEffectBMechanism
SMURF1unknownSLAIN2ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 83 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Activation of BAD and translocation to mitochondria576.1×3e-07
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex567.2×4e-07
SARS-CoV-1 targets host intracellular signalling and regulatory pathways567.2×4e-07
Activation of BH3-only proteins549.6×2e-06
RHO GTPases activate PKNs531.7×2e-05
Intrinsic Pathway for Apoptosis529.3×2e-05
Translocation of SLC2A4 (GLUT4) to the plasma membrane824.7×1e-07
Apoptosis620.1×2e-05

GO biological processes:

GO termPartnersFoldFDR
mitotic spindle organization727.6×3e-06
cerebral cortex development514.9×3e-03
microtubule cytoskeleton organization712.3×4e-04
intracellular protein localization69.1×4e-03
cell division96.0×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance98
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1747 predictions. Top by Δscore:

VariantEffectΔscore
4:48341830:C:Gdonor_gain1.0000
4:48342125:GCTG:Gdonor_gain1.0000
4:48369845:CTAG:Cacceptor_loss1.0000
4:48369846:TAGGC:Tacceptor_loss1.0000
4:48369847:A:ATacceptor_loss1.0000
4:48369848:GGCT:Gacceptor_gain1.0000
4:48377894:A:AGacceptor_gain1.0000
4:48377895:G:GGacceptor_gain1.0000
4:48379687:A:AGacceptor_gain1.0000
4:48379687:AAG:Aacceptor_gain1.0000
4:48379688:A:Gacceptor_gain1.0000
4:48379688:AGGTA:Aacceptor_loss1.0000
4:48379689:G:GCacceptor_loss1.0000
4:48379689:GGT:Gacceptor_gain1.0000
4:48379689:GGTA:Gacceptor_gain1.0000
4:48379844:AGAAA:Adonor_gain1.0000
4:48379845:GAAA:Gdonor_gain1.0000
4:48379845:GAAAG:Gdonor_gain1.0000
4:48379846:AAA:Adonor_gain1.0000
4:48379846:AAAG:Adonor_loss1.0000
4:48379847:AA:Adonor_gain1.0000
4:48379848:AGTA:Adonor_loss1.0000
4:48379849:G:GGdonor_gain1.0000
4:48379850:TAA:Tdonor_loss1.0000
4:48383639:T:Aacceptor_gain1.0000
4:48383642:TGCA:Tacceptor_loss1.0000
4:48383643:GCAG:Gacceptor_loss1.0000
4:48383644:CA:Cacceptor_loss1.0000
4:48383645:A:AGacceptor_gain1.0000
4:48383645:A:Cacceptor_loss1.0000

AlphaMissense

3745 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:48341789:T:AL17Q1.000
4:48341789:T:CL17P1.000
4:48341792:A:CQ18P1.000
4:48341798:T:CL20P1.000
4:48341800:G:AV21M1.000
4:48341810:T:AL24Q1.000
4:48341810:T:CL24P1.000
4:48341819:A:CQ27P1.000
4:48341821:A:GN28D1.000
4:48341831:T:CL31P1.000
4:48379828:T:CL281P1.000
4:48379830:G:CA282P1.000
4:48379831:C:AA282D1.000
4:48379834:G:CR283P1.000
4:48379840:A:CQ285P1.000
4:48382571:T:CL289P1.000
4:48341776:G:AE13K0.999
4:48341779:G:AV14M0.999
4:48341780:T:CV14A0.999
4:48341783:G:CR15P0.999
4:48341789:T:GL17R0.999
4:48341793:G:CQ18H0.999
4:48341793:G:TQ18H0.999
4:48341798:T:AL20Q0.999
4:48341810:T:GL24R0.999
4:48341814:G:CE25D0.999
4:48341814:G:TE25D0.999
4:48341823:C:AN28K0.999
4:48341823:C:GN28K0.999
4:48369910:T:AW151R0.999

dbSNP variants (sampled 300 via entrez): RS1000027730 (4:48380483 A>G), RS10000288 (4:48355510 A>G,T), RS1000090387 (4:48347898 G>A), RS10001054 (4:48406804 A>G,T), RS1000185279 (4:48384355 G>A), RS10003230 (4:48358608 G>A), RS1000335114 (4:48353751 G>A,T), RS10003458 (4:48358814 G>A,T), RS1000399923 (4:48421175 C>T), RS1000414833 (4:48413305 A>G), RS1000433119 (4:48342081 C>A,G), RS10004425 (4:48366942 T>A,C), RS1000457192 (4:48371416 T>A), RS1000458391 (4:48390617 A>G), RS1000521117 (4:48385778 G>A)

Disease associations

OMIM: gene MIM:610492 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST006462_16Uterine fibroids4.000000e-12
GCST007096_77Pulse pressure4.000000e-08
GCST007099_224Systolic blood pressure9.000000e-07
GCST008103_79Bipolar disorder1.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005763pulse pressure measurement
EFO:0006335systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
methylmercuric chlorideaffects cotreatment, decreases expression, increases expression4
Valproic Acidaffects cotreatment, decreases expression, increases expression4
trichostatin Aaffects cotreatment, affects expression, decreases expression3
Tretinoinaffects cotreatment, decreases expression, increases expression3
sodium arseniteaffects cotreatment, decreases expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
FR900359affects phosphorylation1
geldanamycinincreases expression1
triphenyl phosphateaffects expression1
butyraldehydedecreases expression1
benzo(e)pyrenedecreases methylation1
coumarinincreases phosphorylation1
pentanaldecreases expression1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridinedecreases expression1
perfluorooctane sulfonic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression, decreases expression, affects expression1
torcetrapibincreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression, decreases expression, affects expression1
Vorinostatdecreases expression1
Cadmiumdecreases expression, increases abundance1
Caffeineaffects phosphorylation1
Ivermectindecreases expression1
Leaddecreases expression1
Methapyrilenedecreases methylation1
Methotrexateincreases expression1
Dihydrotestosteroneincreases expression1
Thiramincreases expression1
Urethaneincreases expression1
Antirheumatic Agentsincreases 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): uterine corpus leiomyoma