SBSN

Summary

SBSN (suprabasin, HGNC:24950) is a protein-coding gene on chromosome 19q13.12, encoding Suprabasin (Q6UWP8).

Located in extracellular exosome.

Source: NCBI Gene 374897 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 116 total
• MANE Select transcript: NM_001166034

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24950
Approved symbol	SBSN
Name	suprabasin
Location	19q13.12
Locus type	gene with protein product
Status	Approved
Aliases	UNQ698, HLAR698
Ensembl gene	ENSG00000189001
Ensembl biotype	protein_coding
OMIM	609969
Entrez	374897

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000452271, ENST00000518157, ENST00000588674

RefSeq mRNA: 3 — MANE Select: NM_001166034 NM_001166034, NM_001166035, NM_198538

CCDS: CCDS12464, CCDS54253

Canonical transcript exons

ENST00000452271 — 4 exons

Exon	Start	End
ENSE00001625783	35523367	35523533
ENSE00002115619	35526644	35528311
ENSE00003150292	35524711	35524755
ENSE00003175059	35524859	35524924

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 99.88.

FANTOM5 (CAGE): breadth broad, TPM avg 11.7128 / max 3796.3875, expressed in 435 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180533	11.7128	435

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	99.88	gold quality
gingival epithelium	UBERON:0001949	99.84	gold quality
gingiva	UBERON:0001828	99.81	gold quality
lower esophagus mucosa	UBERON:0035834	99.80	gold quality
upper leg skin	UBERON:0004262	99.72	gold quality
mammalian vulva	UBERON:0000997	99.60	gold quality
skin of abdomen	UBERON:0001416	99.58	gold quality
skin of hip	UBERON:0001554	99.39	gold quality
zone of skin	UBERON:0000014	99.36	gold quality
penis	UBERON:0000989	99.32	gold quality
skin of leg	UBERON:0001511	99.17	gold quality
esophagus mucosa	UBERON:0002469	98.87	gold quality
nipple	UBERON:0002030	98.74	gold quality
esophagus squamous epithelium	UBERON:0006920	98.66	gold quality
body of tongue	UBERON:0011876	98.05	gold quality
oral cavity	UBERON:0000167	97.96	gold quality
pharyngeal mucosa	UBERON:0000355	97.72	gold quality
tongue	UBERON:0001723	92.43	gold quality
vagina	UBERON:0000996	86.84	gold quality
superior surface of tongue	UBERON:0007371	84.08	gold quality
esophagus	UBERON:0001043	83.11	gold quality
tonsil	UBERON:0002372	81.75	gold quality
buccal mucosa cell	CL:0002336	81.66	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.44	gold quality
stromal cell of endometrium	CL:0002255	79.25	gold quality
pancreatic ductal cell	CL:0002079	78.89	silver quality
nucleus accumbens	UBERON:0001882	76.98	gold quality
cartilage tissue	UBERON:0002418	76.39	gold quality
mouth mucosa	UBERON:0003729	75.94	gold quality
kidney epithelium	UBERON:0004819	75.85	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	28657.43
E-HCAD-1	yes	3845.99
E-ANND-3	yes	24.97
E-MTAB-10596	no	761.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting SBSN, 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-513B-5P	99.99	69.96	2150
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4504	99.10	69.14	1328
HSA-MIR-12128	96.67	66.98	1471

Literature-anchored findings (GeneRIF, showing 10)

• BORIS induces demethylation of the SBSN CpG island and disruption and activation of chromatin around the SBSN transcription start site, resulting in an increase in SBSN expression. (PMID:22792300)
• These results support suprabasin as novel oncogene candidate in salivary gland adenoid cystic carcinoma. (PMID:23144906)
• Findings suggest that SBSN is involved in the angiogenic potential of tumor endothelial cells (TEC) and may be a novel TEC marker. (PMID:25283635)
• SCARA5 and SBSN shown to have modest effects on cell proliferation or collagen gel contraction and maybe associated with peripheral vein graft patency. (PMID:25935274)
• SBSN expression was observed in human clinical specimens of colon and ovarian carcinomas, as well as in circulating tumour cells and metastases of the 4T1 mouse model. The association of SBSN expression with progressive stages of cancer development indicates its role in cancer evolution and therapy resistance. (PMID:30919591)
• Epidermal SBSN expression was decreased in atopic dermatitis (AD) lesional skin compared to healthy skin. The SBSN serum levels were significantly lower in AD patients than in normal subjects. Study results suggested that SBSN regulates normal epidermal barrierand has an anti-apoptotic activity, and its deficiency is involved in the pathogenesis of AD. (PMID:31399284)
• Aberrantly elevated suprabasin in the bone marrow as a candidate biomarker of advanced disease state in myelodysplastic syndromes. (PMID:32696549)
• Suprabasin-A Review. (PMID:33477529)
• Suprabasin: Role in human cancers and other diseases. (PMID:34775572)
• Extracellular vesicles-transferred SBSN drives glioma aggressiveness by activating NF-kappaB via ANXA1-dependent ubiquitination of NEMO. (PMID:36316443)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Sbsn	ENSMUSG00000046056
rattus_norvegicus	Sbsn	ENSRNOG00000021015

Protein

Protein identifiers

Suprabasin — Q6UWP8 (reviewed: Q6UWP8)

All UniProt accessions (2): K7ESC4, Q6UWP8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Tissue specificity. Detected in thymus, uterus and esophagus.

Induction. Up-regulated in differentiating keratinocytes.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UWP8-1	1	yes
Q6UWP8-2	2

RefSeq proteins (3): NP_001159506, NP_001159507, NP_940940 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024153	Suprabasin	Family
IPR049502	SBSN_GxHH_rpt	Repeat

Pfam: PF21009

UniProt features (17 total): compositionally biased region 5, sequence conflict 4, region of interest 4, signal peptide 1, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UWP8-F1	51.59	0.00

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-9725554	Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin
R-HSA-1266738	Developmental Biology
R-HSA-9734767	Developmental Cell Lineages

MSigDB gene sets: 59 (showing top): GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, TTGCWCAAY_CEBPB_02, CEBPB_01, TGANTCA_AP1_C, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, CEBPB_02, AP1_Q6_01, MIR12123, MIR4504, GSE10273_HIGH_IL7_VS_HIGH_IL7_AND_IRF4_IN_IRF4_8_NULL_PRE_BCELL_UP, GSE13306_TREG_VS_TCONV_LAMINA_PROPRIA_UP, BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_UP, BLANCO_MELO_BETA_INTERFERON_TREATED_BRONCHIAL_EPITHELIAL_CELLS_DN, GSE14769_UNSTIM_VS_20MIN_LPS_BMDM_UP

GO Biological Process (0):

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

GO Cellular Component (2): extracellular exosome (GO:0070062), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Developmental Cell Lineages of the Integumentary System	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
extracellular vesicle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1859 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SBSN	TGM3	Q08188	819
SBSN	KRTDAP	P60985	790
SBSN	DMKN	Q6E0U4	683
SBSN	TGM2	P21980	634
SBSN	PRKCA	P17252	560
SBSN	GGCT	O75223	501
SBSN	KRT2	P35908	489
SBSN	SERPINB12	Q96P63	460
SBSN	CLU	P10909	455
SBSN	LGALS7B	P47929	452
SBSN	CNFN	Q9BYD5	450
SBSN	ORM1	P02763	447
SBSN	SCEL	O95171	447
SBSN	CRCT1	Q9UGL9	447
SBSN	SAA1	P02735	447

IntAct

128 interactions, top by confidence:

A	B	Type	Score
ANAPC5	CDC27	psi-mi:“MI:0914”(association)	0.810
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CCNC	MED19	psi-mi:“MI:0914”(association)	0.640
ALDH3A1	RCCD1	psi-mi:“MI:0914”(association)	0.640
CFAP298	PEX7	psi-mi:“MI:0914”(association)	0.620
ZSCAN12	A2ML1	psi-mi:“MI:0914”(association)	0.530
GMCL1	A2ML1	psi-mi:“MI:0914”(association)	0.530
TBC1D22B	A2ML1	psi-mi:“MI:0914”(association)	0.530
FTH1	A2ML1	psi-mi:“MI:0914”(association)	0.530
NDUFS5	NDUFS4	psi-mi:“MI:0914”(association)	0.530
DTL	DNAJA2	psi-mi:“MI:0914”(association)	0.530
MMRN1	CTSV	psi-mi:“MI:0914”(association)	0.530
TOX4	ALOX12B	psi-mi:“MI:0914”(association)	0.530
PHAF1	PSMG1	psi-mi:“MI:0914”(association)	0.530
STK16	FLG	psi-mi:“MI:0914”(association)	0.530
RAB9B	CHM	psi-mi:“MI:0914”(association)	0.530
CUL1	HAL	psi-mi:“MI:0914”(association)	0.530
INPP5A	RCCD1	psi-mi:“MI:0914”(association)	0.530
CDC42EP4	SEPTIN6	psi-mi:“MI:0914”(association)	0.530
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
SBSN	SLITRK3	psi-mi:“MI:0915”(physical association)	0.400
Haus1	LTF	psi-mi:“MI:0914”(association)	0.350
Tnks	SDC2	psi-mi:“MI:0914”(association)	0.350
Gsk3b	SYNPO2	psi-mi:“MI:0914”(association)	0.350

BioGRID (135): SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Proximity Label-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS), SBSN (Affinity Capture-MS)

ESM2 similar proteins: A0A0D1CKI0, A0A0H3K686, A0A6B9KZ90, A6QQF6, D2K835, O24006, O88492, P01357, P02674, P02894, P02976, P04922, P05222, P05226, P05995, P08672, P08673, P08674, P08675, P08676, P08677, P08798, P0A015, P0DRJ4, P13673, P13826, P14606, P38507, P81592, P99134, Q03110, Q03646, Q09180, Q1ELU4, Q1ELU5, Q28201, Q28298, Q29428, Q42626, Q42627

Diamond homologs: A6QQF6, Q6UWP8, Q8CIT9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	93
Likely benign	15
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

574 predictions. Top by Δscore:

Variant	Effect	Δscore
19:35524706:CTCA:C	donor_loss	1.0000
19:35524707:TCA:T	donor_loss	1.0000
19:35524708:CACC:C	donor_loss	1.0000
19:35524709:A:AC	donor_gain	1.0000
19:35524709:AC:A	donor_gain	1.0000
19:35524709:ACCC:A	donor_loss	1.0000
19:35524709:ACCCT:A	donor_gain	1.0000
19:35524710:C:CC	donor_gain	1.0000
19:35524710:C:CT	donor_loss	1.0000
19:35524710:CC:C	donor_gain	1.0000
19:35524710:CCCT:C	donor_gain	1.0000
19:35524710:CCCTC:C	donor_gain	1.0000
19:35524751:GAGGC:G	acceptor_gain	1.0000
19:35524752:AGGC:A	acceptor_gain	1.0000
19:35524752:AGGCC:A	acceptor_loss	1.0000
19:35524753:GGC:G	acceptor_gain	1.0000
19:35524754:GC:G	acceptor_gain	1.0000
19:35524754:GCC:G	acceptor_loss	1.0000
19:35524755:CC:C	acceptor_gain	1.0000
19:35524756:C:CC	acceptor_gain	1.0000
19:35524756:CTG:C	acceptor_loss	1.0000
19:35524757:T:C	acceptor_loss	1.0000
19:35524760:A:T	acceptor_gain	1.0000
19:35524761:A:AC	acceptor_gain	1.0000
19:35524764:C:CT	acceptor_gain	1.0000
19:35524854:CTTA:C	donor_loss	1.0000
19:35524857:A:AC	donor_gain	1.0000
19:35524857:AC:A	donor_gain	1.0000
19:35524857:ACC:A	donor_gain	1.0000
19:35524857:ACCCC:A	donor_loss	1.0000

AlphaMissense

3919 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:35528101:C:G	A61P	0.991
19:35528109:A:G	I58T	0.990
19:35528134:C:G	A50P	0.988
19:35528100:G:T	A61D	0.987
19:35528121:A:G	I54T	0.987
19:35528109:A:C	I58S	0.984
19:35528121:A:C	I54S	0.983
19:35528109:A:T	I58N	0.977
19:35528121:A:T	I54N	0.977
19:35528130:A:G	L51P	0.977
19:35528155:C:G	A43P	0.973
19:35528133:G:T	A50D	0.968
19:35528163:A:G	L40P	0.954
19:35528067:A:G	L72P	0.936
19:35524735:G:C	F575L	0.935
19:35524735:G:T	F575L	0.935
19:35524737:A:G	F575L	0.935
19:35528179:C:A	G35W	0.932
19:35528113:C:G	G57R	0.931
19:35528113:C:T	G57R	0.931
19:35528167:C:A	G39W	0.930
19:35528151:T:A	E44V	0.929
19:35528154:G:T	A43E	0.929
19:35528175:A:G	I36T	0.929
19:35528130:A:T	L51Q	0.927
19:35524716:A:G	W582R	0.926
19:35524716:A:T	W582R	0.926
19:35528085:T:A	E66V	0.921
19:35528112:C:T	G57E	0.919
19:35528117:G:C	N55K	0.918

dbSNP variants (sampled 300 via entrez): RS1000166337 (19:35523335 T>C,G), RS1000315720 (19:35528513 C>T), RS1000705043 (19:35523134 T>C), RS1001724351 (19:35524339 G>A), RS1001958594 (19:35525597 T>TC), RS1002502960 (19:35528783 G>A,T), RS1002882009 (19:35525566 T>A), RS1004310287 (19:35525827 C>T), RS1004482083 (19:35526043 C>A,T), RS1005919636 (19:35523645 C>T), RS1006174909 (19:35529487 C>T), RS1006207496 (19:35529839 G>A), RS1006357257 (19:35524016 C>A), RS1006841229 (19:35524285 A>G), RS1007988328 (19:35526467 C>T)

Disease associations

OMIM: gene MIM:609969 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST90002400_282	Plateletcrit	4.000000e-20
GCST90002402_560	Platelet count	5.000000e-20

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007985	platelet crit
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	2
butyraldehyde	increases expression	2
pentanal	increases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
aristolochic acid I	increases expression	1
bisphenol A	increases expression	1
sodium arsenate	decreases expression, increases abundance	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression	1
terbufos	increases methylation	1
versicolorin A	increases expression	1
caprylic aldehyde	increases expression	1
4-aminophenylarsenoxide	decreases reaction, affects binding	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
heptanal	increases expression	1
thrombin receptor-activating peptide SFLLRNPNDKY	decreases reaction, increases secretion	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	increases expression, decreases reaction	1
licochalcone B	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Arsenic	decreases expression, increases abundance	1
Aspirin	increases secretion, decreases reaction	1
Vehicle Emissions	decreases reaction, increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	increases expression	1
Fonofos	increases methylation	1
Furaldehyde	affects cotreatment, increases expression	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Parathion	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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