SLAIN1

Summary

SLAIN1 (SLAIN family member 1, HGNC:26387) is a protein-coding gene on chromosome 13q22.3, encoding SLAIN motif-containing protein 1 (Q8ND83). Microtubule plus-end tracking protein that might be involved in the regulation of cytoplasmic microtubule dynamics, microtubule organization and microtubule elongation.

Predicted to be involved in cytoplasmic microtubule organization; microtubule nucleation; and positive regulation of microtubule polymerization. Predicted to be located in microtubule plus-end.

Source: NCBI Gene 122060 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 67 total — 1 pathogenic
• MANE Select transcript: NM_001242868

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26387
Approved symbol	SLAIN1
Name	SLAIN family member 1
Location	13q22.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30046
Ensembl gene	ENSG00000139737
Ensembl biotype	protein_coding
OMIM	610491
Entrez	122060

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 17 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000267219, ENST00000314070, ENST00000351546, ENST00000358679, ENST00000377236, ENST00000418532, ENST00000422114, ENST00000441784, ENST00000442759, ENST00000446759, ENST00000462234, ENST00000465831, ENST00000466548, ENST00000474663, ENST00000481614, ENST00000488699, ENST00000496045, ENST00000705543

RefSeq mRNA: 11 — MANE Select: NM_001242868 NM_001040153, NM_001242868, NM_001242869, NM_001242870, NM_001242871, NM_001366665, NM_001366666, NM_001411026, NM_001412123, NM_001412125, NM_144595

CCDS: CCDS31995, CCDS55901, CCDS73588, CCDS73589, CCDS91820, CCDS91821, CCDS9460

Canonical transcript exons

ENST00000418532 — 7 exons

Exon	Start	End
ENSE00001670715	77697687	77698539
ENSE00003889262	77744283	77744432
ENSE00003890808	77760828	77761110
ENSE00003893133	77746514	77746855
ENSE00003895962	77753203	77753358
ENSE00003896020	77763145	77764229
ENSE00003896191	77719532	77719671

Expression profiles

Bgee: expression breadth ubiquitous, 216 present calls, max score 99.28.

FANTOM5 (CAGE): breadth broad, TPM avg 13.9963 / max 976.9348, expressed in 850 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135514	7.4792	638
135515	3.5529	732
135524	1.6415	91
135520	0.3933	69
135519	0.2687	60
135525	0.1884	61
135526	0.1829	73
135521	0.1415	59
135523	0.1252	60
135522	0.0226	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	99.28	gold quality
spinal cord	UBERON:0002240	99.17	gold quality
corpus callosum	UBERON:0002336	99.11	gold quality
inferior vagus X ganglion	UBERON:0005363	98.03	gold quality
substantia nigra	UBERON:0002038	97.68	gold quality
midbrain	UBERON:0001891	97.43	gold quality
subthalamic nucleus	UBERON:0001906	97.33	gold quality
embryo	UBERON:0000922	97.30	gold quality
ganglionic eminence	UBERON:0004023	97.30	gold quality
ventricular zone	UBERON:0003053	97.28	gold quality
endothelial cell	CL:0000115	97.15	gold quality
Brodmann (1909) area 46	UBERON:0006483	96.76	gold quality
putamen	UBERON:0001874	96.55	gold quality
medulla oblongata	UBERON:0001896	96.52	gold quality
lateral globus pallidus	UBERON:0002476	96.45	gold quality
caudate nucleus	UBERON:0001873	96.38	gold quality
substantia nigra pars reticulata	UBERON:0001966	96.32	gold quality
amygdala	UBERON:0001876	96.27	gold quality
Ammon’s horn	UBERON:0001954	96.13	gold quality
cortical plate	UBERON:0005343	95.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.87	gold quality
hypothalamus	UBERON:0001898	95.82	gold quality
dorsal plus ventral thalamus	UBERON:0001897	95.73	gold quality
superior vestibular nucleus	UBERON:0007227	95.48	gold quality
nucleus accumbens	UBERON:0001882	95.02	gold quality
pons	UBERON:0000988	94.96	gold quality
prefrontal cortex	UBERON:0000451	94.77	gold quality
globus pallidus	UBERON:0001875	94.77	gold quality
substantia nigra pars compacta	UBERON:0001965	94.74	gold quality
telencephalon	UBERON:0001893	94.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	82.88
E-HCAD-25	yes	60.23
E-GEOD-84465	yes	11.04
E-ANND-3	yes	8.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

136 targeting SLAIN1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502

Literature-anchored findings (GeneRIF, showing 1)

• Expressed at the stem cell and epiblast stages of embryonic stem cell differentiation. (PMID:16546155)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	slain1a	ENSDARG00000019185
mus_musculus	Slain1	ENSMUSG00000055717
rattus_norvegicus	Slain1	ENSRNOG00000024125

Paralogs (1): SLAIN2 (ENSG00000109171)

Protein

Protein identifiers

SLAIN motif-containing protein 1 — Q8ND83 (reviewed: Q8ND83)

All UniProt accessions (14): Q8ND83, A0A0A0MSS3, A0A0C4DFN6, A0A994J5K0, B7Z326, C9JAC5, C9JD09, C9JP03, C9JUW9, Q5T6P1, Q5T6P2, Q5T6P5, X6RDJ2, X6RGK9

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule plus-end tracking protein that might be involved in the regulation of cytoplasmic microtubule dynamics, microtubule organization and microtubule elongation.

Subunit / interactions. Interacts with MAPRE1, MAPRE2, MAPRE3 and CKAP5. Interacts with ZDHHC17 (via ANK repeats).

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Expressed in embryonic stem cells. Expressed in brain.

Similarity. Belongs to the SLAIN motif-containing family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8ND83-1	1	yes
Q8ND83-2	2
Q8ND83-3	3
Q8ND83-4	4

RefSeq proteins (11): NP_001035243, NP_001229797, NP_001229798, NP_001229799, NP_001229800, NP_001353594, NP_001353595, NP_001397955, NP_001399052, NP_001399054, NP_653196 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026179	Slain	Family

Pfam: PF15301

UniProt features (24 total): compositionally biased region 9, region of interest 5, splice variant 4, modified residue 3, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8ND83-F1	54.80	0.10

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): 243, 471, 543

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 193 (showing top): GCM_MAP4K4, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, GCM_PTPRD, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, TGCACTT_MIR519C_MIR519B_MIR519A, TTTGTAG_MIR520D, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_MICROTUBULE_NUCLEATION, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_MICROTUBULE_POLYMERIZATION_OR_DEPOLYMERIZATION, GOBP_REGULATION_OF_MICROTUBULE_POLYMERIZATION, GATA1_01

GO Biological Process (3): microtubule nucleation (GO:0007020), positive regulation of microtubule polymerization (GO:0031116), cytoplasmic microtubule organization (GO:0031122)

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

GO Cellular Component (3): cytoskeleton (GO:0005856), cytoplasm (GO:0005737), microtubule plus-end (GO:0035371)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule cytoskeleton organization	2
microtubule polymerization	2
positive regulation of microtubule polymerization or depolymerization	1
regulation of microtubule polymerization	1
positive regulation of protein polymerization	1
positive regulation of supramolecular fiber organization	1
supramolecular fiber organization	1
binding	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1
microtubule end	1

Protein interactions and networks

STRING

971 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLAIN1	DAZAP2	Q15038	507
SLAIN1	TOB2	Q14106	490
SLAIN1	CKAP5	Q14008	474
SLAIN1	TMEM161B	Q8NDZ6	357
SLAIN1	MINDY2	Q8NBR6	341
SLAIN1	DOP1B	Q9Y3R5	338
SLAIN1	NBPF9	P0DPF3	327
SLAIN1	ANKRD12	Q6UB98	323
SLAIN1	RWDD2A	Q9UIY3	322
SLAIN1	SPTY2D1	Q68D10	312
SLAIN1	C22orf39	Q6P5X5	308
SLAIN1	KCTD18	Q6PI47	306
SLAIN1	EDNRB	P24530	299
SLAIN1	TMEM183A	Q8IXX5	298
SLAIN1	OR6K6	Q8NGW6	297

IntAct

143 interactions, top by confidence:

A	B	Type	Score
CKAP5	TACC1	psi-mi:“MI:0914”(association)	0.800
SLAIN1	FHL3	psi-mi:“MI:0915”(physical association)	0.720
FHL3	SLAIN1	psi-mi:“MI:0915”(physical association)	0.720
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
PSMA3	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
SLAIN1	PSMA3	psi-mi:“MI:0915”(physical association)	0.560
ARMC7	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
FHL2	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
CARD9	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
HSF2BP	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
DDX6	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
PAX9	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
AIRIM	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
PATZ1	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
LMO3	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
GOLGA1	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
ARHGEF5	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
TFAP2D	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
COX5B	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
FRS3	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
TBC1D22B	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
KIF9	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560
CRACR2A	SLAIN1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (108): SLAIN1 (Two-hybrid), SLAIN1 (Two-hybrid), SLAIN1 (Affinity Capture-MS), SLAIN1 (Affinity Capture-MS), SLAIN1 (Affinity Capture-MS), SLAIN1 (Affinity Capture-MS), SLAIN1 (Biochemical Activity), SLAIN1 (Affinity Capture-MS), SLAIN1 (Affinity Capture-MS), MAPRE1 (Two-hybrid), MAPRE3 (Two-hybrid), DMRTB1 (Two-hybrid), AKAP9 (Two-hybrid), RBM14 (Two-hybrid), NDEL1 (Two-hybrid)

ESM2 similar proteins: A0A088MLT8, A2AQ25, B3KU38, B5DF41, E9PSK7, O15079, O35274, P0DPB3, P0DPB4, P12755, P49140, P85299, Q0D2I5, Q14DQ1, Q1LY51, Q3B7M3, Q3SYW5, Q4KMA0, Q4R3X1, Q50H33, Q5F3L9, Q5FVG6, Q5RD40, Q5XKK7, Q60698, Q6ZNC4, Q6ZUS6, Q6ZWB6, Q80U23, Q80U62, Q80XA6, Q812A5, Q86YI8, Q8BXL9, Q8K2W6, Q8ND83, Q8NFH8, Q8QFX1, Q8TEK3, Q924W7

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

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 76 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:

Pathway	Partners	Fold	FDR
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand	5	21.0×	2e-04
Translocation of SLC2A4 (GLUT4) to the plasma membrane	6	20.1×	7e-05
Kinesins	5	19.4×	2e-04
The role of GTSE1 in G2/M progression after G2 checkpoint	5	17.5×	2e-04
Golgi-to-ER retrograde transport	6	17.3×	8e-05
Loss of Nlp from mitotic centrosomes	5	17.2×	2e-04
Loss of proteins required for interphase microtubule organization from the centrosome	5	17.2×	2e-04
AURKA Activation by TPX2	5	16.6×	2e-04

GO biological processes:

GO term	Partners	Fold	FDR
mitotic spindle organization	6	24.0×	7e-05
microtubule cytoskeleton organization	7	12.5×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	45
Likely benign	5
Benign	4

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2685473	GRCh37/hg19 13q21.33-33.1(chr13:73132193-104595598)x1	Pathogenic

SpliceAI

776 predictions. Top by Δscore:

Variant	Effect	Δscore
13:77744278:TTCA:T	acceptor_loss	1.0000
13:77744281:A:AG	acceptor_gain	1.0000
13:77744282:G:GG	acceptor_gain	1.0000
13:77744282:G:GT	acceptor_loss	1.0000
13:77744282:GGTT:G	acceptor_gain	1.0000
13:77744282:GGTTA:G	acceptor_gain	1.0000
13:77744428:AGAAA:A	donor_gain	1.0000
13:77744429:GAAA:G	donor_gain	1.0000
13:77744429:GAAAG:G	donor_gain	1.0000
13:77744430:A:T	donor_gain	1.0000
13:77744430:AAAGT:A	donor_loss	1.0000
13:77744431:AA:A	donor_gain	1.0000
13:77744431:AAG:A	donor_loss	1.0000
13:77744432:AG:A	donor_loss	1.0000
13:77744433:G:GC	donor_loss	1.0000
13:77744433:G:GG	donor_gain	1.0000
13:77744434:TATGT:T	donor_loss	1.0000
13:77753198:TCCA:T	acceptor_loss	1.0000
13:77753200:CA:C	acceptor_loss	1.0000
13:77753201:A:AG	acceptor_gain	1.0000
13:77753202:G:GC	acceptor_loss	1.0000
13:77753202:G:GG	acceptor_gain	1.0000
13:77753202:GATA:G	acceptor_gain	1.0000
13:77753202:GATAA:G	acceptor_gain	1.0000
13:77753354:TTGTA:T	donor_gain	1.0000
13:77753356:GTA:G	donor_gain	1.0000
13:77753357:TA:T	donor_gain	1.0000
13:77753358:AG:A	donor_loss	1.0000
13:77753359:G:GG	donor_gain	1.0000
13:77753359:GTG:G	donor_loss	1.0000

AlphaMissense

3779 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:77698008:T:C	L32P	1.000
13:77698017:T:C	L35P	1.000
13:77698029:T:C	L39P	1.000
13:77744385:T:C	L268S	1.000
13:77744403:T:A	V274D	1.000
13:77744414:G:C	A278P	1.000
13:77744415:C:A	A278D	1.000
13:77744418:G:C	R279P	1.000
13:77744421:T:C	L280P	1.000
13:77698019:G:A	V36M	0.999
13:77698023:G:C	R37P	0.999
13:77698029:T:A	L39Q	0.999
13:77698038:A:C	Q42P	0.999
13:77698040:A:G	N43D	0.999
13:77698050:T:C	L46P	0.999
13:77744390:G:C	D270H	0.999
13:77744391:A:C	D270A	0.999
13:77744391:A:G	D270G	0.999
13:77744391:A:T	D270V	0.999
13:77744394:T:C	L271P	0.999
13:77744399:G:C	D273H	0.999
13:77744399:G:T	D273Y	0.999
13:77744400:A:C	D273A	0.999
13:77744400:A:G	D273G	0.999
13:77744400:A:T	D273V	0.999
13:77744406:A:C	Q275P	0.999
13:77744409:T:A	I276N	0.999
13:77744409:T:C	I276T	0.999
13:77744409:T:G	I276S	0.999
13:77744424:A:C	Q281P	0.999

dbSNP variants (sampled 300 via entrez): RS1000007779 (13:77721186 G>A,T), RS1000023798 (13:77742916 T>C), RS1000032841 (13:77697360 C>G,T), RS1000054768 (13:77742592 G>A), RS1000062170 (13:77708613 A>T), RS1000074448 (13:77743220 C>T), RS1000265127 (13:77718078 A>G), RS1000296244 (13:77717745 T>C), RS1000357845 (13:77749529 A>C,G), RS1000383115 (13:77756215 A>G), RS1000414581 (13:77738771 C>G), RS1000431779 (13:77708838 A>C), RS1000446440 (13:77697107 T>C,G), RS1000527157 (13:77756442 G>A,C), RS1000556418 (13:77737544 T>A)

Disease associations

OMIM: gene MIM:610491 | 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):

Study	Trait	p-value
GCST004412_10	Craniofacial microsomia	8.000000e-06
GCST006988_7	Blond vs. brown/black hair color	7.000000e-145
GCST006989_9	Brown vs. black hair color	3.000000e-34
GCST009391_90	Metabolite levels	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0003924	hair color

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	affects expression, decreases methylation, increases expression	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
potassium chromate(VI)	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
2,2’,4,4’,5-brominated diphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases methylation	1
NSC 689534	affects binding, decreases expression	1
(+)-JQ1 compound	increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Acetaminophen	increases expression	1
Cadmium	increases abundance, increases expression	1
Copper	decreases expression, affects binding	1
Doxorubicin	decreases expression	1
Endosulfan	increases expression	1
Estradiol	affects cotreatment, decreases expression	1
Formaldehyde	decreases expression	1
Gallic Acid	increases expression	1
Methyl Methanesulfonate	decreases expression	1
Progesterone	decreases expression	1
Tretinoin	decreases expression	1
Vanadates	decreases expression	1

Clinical trials (associated diseases)

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