SBSPON

Summary

SBSPON (somatomedin B and thrombospondin type 1 domain containing, HGNC:30362) is a protein-coding gene on chromosome 8q21.11, encoding Somatomedin-B and thrombospondin type-1 domain-containing protein (Q8IVN8).

Predicted to be an extracellular matrix structural constituent. Located in collagen-containing extracellular matrix.

Source: NCBI Gene 157869 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_153225

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30362
Approved symbol	SBSPON
Name	somatomedin B and thrombospondin type 1 domain containing
Location	8q21.11
Locus type	gene with protein product
Status	Approved
Aliases	RPESP
Ensembl gene	ENSG00000164764
Ensembl biotype	protein_coding
OMIM	621005
Entrez	157869

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000297354, ENST00000519697, ENST00000964790

RefSeq mRNA: 1 — MANE Select: NM_153225 NM_153225

CCDS: CCDS43747

Canonical transcript exons

ENST00000297354 — 5 exons

Exon	Start	End
ENSE00001251013	73092854	73093172
ENSE00001945819	73064543	73067458
ENSE00003494427	73081019	73081213
ENSE00003500679	73071780	73071870
ENSE00003609345	73069805	73069981

Expression profiles

Bgee: expression breadth ubiquitous, 229 present calls, max score 96.56.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0937 / max 191.8258, expressed in 271 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
93582	2.0937	271

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
germinal epithelium of ovary	UBERON:0001304	96.56	gold quality
saphenous vein	UBERON:0007318	93.91	gold quality
tibial nerve	UBERON:0001323	92.37	gold quality
right coronary artery	UBERON:0001625	90.63	gold quality
left coronary artery	UBERON:0001626	89.66	gold quality
popliteal artery	UBERON:0002250	89.46	gold quality
tibial artery	UBERON:0007610	89.45	gold quality
artery	UBERON:0001637	89.40	gold quality
coronary artery	UBERON:0001621	89.27	gold quality
mucosa of stomach	UBERON:0001199	89.12	gold quality
aorta	UBERON:0000947	86.66	gold quality
sural nerve	UBERON:0015488	86.19	gold quality
trigeminal ganglion	UBERON:0001675	85.69	gold quality
dorsal root ganglion	UBERON:0000044	85.32	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.01	gold quality
caput epididymis	UBERON:0004358	84.47	gold quality
cauda epididymis	UBERON:0004360	84.39	gold quality
descending thoracic aorta	UBERON:0002345	84.38	gold quality
superficial temporal artery	UBERON:0001614	83.81	gold quality
seminal vesicle	UBERON:0000998	83.28	gold quality
thoracic aorta	UBERON:0001515	83.08	gold quality
ascending aorta	UBERON:0001496	82.91	gold quality
sperm	CL:0000019	82.56	gold quality
urinary bladder	UBERON:0001255	81.23	gold quality
fundus of stomach	UBERON:0001160	81.06	gold quality
body of stomach	UBERON:0001161	80.91	gold quality
left uterine tube	UBERON:0001303	80.71	gold quality
stomach	UBERON:0000945	80.20	gold quality
male germ cell	CL:0000015	79.83	gold quality
urethra	UBERON:0000057	79.60	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-10662	yes	506.17
E-ENAD-20	yes	166.26
E-ANND-3	yes	16.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

143 targeting SBSPON, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
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-548J-3P	99.94	72.61	4881
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-335-3P	99.93	73.36	4958

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	SBSPON	ENSDARG00000110160
mus_musculus	Sbspon	ENSMUSG00000032719
rattus_norvegicus	Sbspon	ENSRNOG00000007258
drosophila_melanogaster	vex	FBGN0259241
caenorhabditis_elegans		WBGENE00011269

Protein

Protein identifiers

Somatomedin-B and thrombospondin type-1 domain-containing protein — Q8IVN8 (reviewed: Q8IVN8)

Alternative names: RPE-spondin

All UniProt accessions (1): Q8IVN8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Detected in aorta extracellular matrix (at protein level).

Similarity. Belongs to the thrombospondin family.

RefSeq proteins (1): NP_694957* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000884	TSP1_rpt	Repeat
IPR001212	Somatomedin_B_dom	Domain
IPR036024	Somatomedin_B-like_dom_sf	Homologous_superfamily
IPR036383	TSP1_rpt_sf	Homologous_superfamily
IPR039942	SBSPO	Family
IPR044004	TSP1_spondin_dom	Domain
IPR056801	SBSPON_C	Domain

Pfam: PF19028, PF25031

UniProt features (14 total): disulfide bond 7, sequence variant 2, domain 2, signal peptide 1, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IVN8-F1	87.17	0.68

Functional residue map

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

Disulfide bonds (7): 56–62, 63–70, 28–52, 28–36, 36–70, 50–63, 50–52

Glycosylation sites (1): 227

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-5083635	Defective B3GALTL causes PpS
R-HSA-5173214	O-glycosylation of TSR domain-containing proteins
R-HSA-1643685	Disease
R-HSA-3781865	Diseases of glycosylation
R-HSA-3906995	Diseases associated with O-glycosylation of proteins
R-HSA-392499	Metabolism of proteins
R-HSA-5173105	O-linked glycosylation
R-HSA-5668914	Diseases of metabolism
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 129 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, WTGAAAT_UNKNOWN, NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON, TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN, RICKMAN_HEAD_AND_NECK_CANCER_A, TGGNNNNNNKCCAR_UNKNOWN, HAND1E47_01, VECCHI_GASTRIC_CANCER_EARLY_DN, BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP, NOUZOVA_METHYLATED_IN_APL

GO Biological Process (0):

GO Molecular Function (1): extracellular matrix structural constituent (GO:0005201)

GO Cellular Component (2): extracellular matrix (GO:0031012), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
Diseases associated with O-glycosylation of proteins	1
O-linked glycosylation	1
Diseases of metabolism	1
Diseases of glycosylation	1
Post-translational protein modification	1
Disease	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
structural molecule activity	1
extracellular matrix	1
external encapsulating structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1959 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SBSPON	DPY19L3	Q6ZPD9	446
SBSPON	FAM229B	Q4G0N7	433
SBSPON	C2orf68	Q2NKX9	393
SBSPON	MEGF6	O75095	356
SBSPON	ABI3BP	Q7Z7G0	344
SBSPON	ITIH6	Q6UXX5	333
SBSPON	EIF1AD	Q8N9N8	329
SBSPON	RHBDD2	Q6NTF9	327
SBSPON	TNS4	Q8IZW8	321
SBSPON	CABCOCO1	Q8IVU9	295
SBSPON	LTBP4	Q8N2S1	295
SBSPON	LYPD5	Q6UWN5	288
SBSPON	ZNF175	Q9Y473	286
SBSPON	CYSTM1	Q9H1C7	278
SBSPON	LMCD1	Q9NZU5	277

IntAct

3 interactions, top by confidence:

A	B	Type	Score
SBSPON	ZNF609	psi-mi:“MI:0914”(association)	0.530

BioGRID (6): ZNF609 (Affinity Capture-MS), ZNF703 (Affinity Capture-MS), GFER (Affinity Capture-MS), ZNF703 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS), GFER (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTW7, A0A1D5NSK0, A0A1L8HYT7, A0A286YEC0, G7PWZ3, O77755, O88959, P0C0K7, P17490, P23276, P43021, P51882, P59509, P59996, P70505, Q02853, Q04912, Q04962, Q04997, Q0V8J4, Q0VAY3, Q17R55, Q3U435, Q499S5, Q4R7Z5, Q58Y75, Q62190, Q6MG64, Q76MJ5, Q7TN88, Q7Z442, Q80W65, Q8BMN4, Q8CJH3, Q8IVN8, Q8VCS0, Q91X21, Q96KR4, Q96PQ0, Q96S42

Diamond homologs: A7MBS7, B3EWY9, B3EWZ8, Q1RMU1, Q2MKA7, Q3UPR9, Q5R328, Q5R7Y0, Q69Z28, Q69ZU6, Q6P4U0, Q8BMS2, Q8IVN8, Q8TE57, Q9BUD6, Q9C0I4, Q9UPZ6, Q9WV75, Q9Z132, A2VE04, C5IAW9, D3YXG0, E9Q6D8, F1LW30, G5ECS8, O08721, O08747, O60241, O60242, O95185, P07996, P11680, P27918, P35440, P35441, P35442, P35446, P35447, P48770, P59384

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

815 predictions. Top by Δscore:

Variant	Effect	Δscore
8:73071782:AGCAT:A	donor_gain	1.0000
8:73092863:C:CA	donor_gain	1.0000
8:73069803:AC:A	donor_gain	0.9900
8:73069804:CC:C	donor_gain	0.9900
8:73069982:C:CC	acceptor_gain	0.9900
8:73071786:T:TA	donor_gain	0.9900
8:73071871:C:CC	acceptor_gain	0.9900
8:73081061:C:CA	donor_gain	0.9900
8:73086785:A:AC	donor_gain	0.9900
8:73086786:C:CC	donor_gain	0.9900
8:73092849:CCCA:C	donor_loss	0.9900
8:73092850:CCAC:C	donor_loss	0.9900
8:73092851:CA:C	donor_loss	0.9900
8:73092852:A:AG	donor_loss	0.9900
8:73092853:C:CT	donor_loss	0.9900
8:73069799:TCTTA:T	donor_loss	0.9800
8:73069800:CTTAC:C	donor_loss	0.9800
8:73069801:TTACC:T	donor_loss	0.9800
8:73069802:T:TA	donor_loss	0.9800
8:73069803:A:AC	donor_gain	0.9800
8:73069803:A:T	donor_loss	0.9800
8:73069804:C:CC	donor_gain	0.9800
8:73069804:CCCAT:C	donor_gain	0.9800
8:73069978:GTATC:G	acceptor_loss	0.9800
8:73069979:TATC:T	acceptor_loss	0.9800
8:73069980:ATC:A	acceptor_loss	0.9800
8:73069981:TCTAC:T	acceptor_loss	0.9800
8:73069982:C:A	acceptor_loss	0.9800
8:73069983:T:G	acceptor_loss	0.9800
8:73071778:AC:A	donor_gain	0.9800

AlphaMissense

1719 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:73067404:C:A	W244C	0.999
8:73067404:C:G	W244C	0.999
8:73067440:C:A	W232C	0.999
8:73067440:C:G	W232C	0.999
8:73081188:C:A	W80C	0.999
8:73081188:C:G	W80C	0.999
8:73069909:C:A	W191C	0.998
8:73069909:C:G	W191C	0.998
8:73081179:C:A	W83C	0.998
8:73081179:C:G	W83C	0.998
8:73067347:A:C	F263L	0.997
8:73067347:A:T	F263L	0.997
8:73067349:A:G	F263L	0.997
8:73067417:C:G	C240S	0.997
8:73067418:A:T	C240S	0.997
8:73069832:C:G	C217S	0.997
8:73069833:A:T	C217S	0.997
8:73069967:A:C	F172C	0.997
8:73067348:A:C	F263C	0.996
8:73067406:A:G	W244R	0.996
8:73067406:A:T	W244R	0.996
8:73069967:A:G	F172S	0.996
8:73067442:A:G	W232R	0.995
8:73067442:A:T	W232R	0.995
8:73069868:C:G	C205S	0.995
8:73069869:A:T	C205S	0.995
8:73069966:A:C	F172L	0.995
8:73069966:A:T	F172L	0.995
8:73069968:A:G	F172L	0.995
8:73067348:A:G	F263S	0.994

dbSNP variants (sampled 300 via entrez): RS1000025426 (8:73073038 T>C), RS1000056716 (8:73073375 G>A), RS1000187619 (8:73074492 A>G), RS1000243154 (8:73067072 G>T), RS1000365322 (8:73067987 C>T), RS1000698405 (8:73066787 G>A), RS1000713731 (8:73073222 G>T), RS1000791938 (8:73065728 G>A,C), RS1000832924 (8:73074694 T>C), RS1000891272 (8:73084798 A>T), RS1000948949 (8:73090950 T>C), RS1000980725 (8:73068596 C>T), RS1000993547 (8:73085769 A>G), RS1001003561 (8:73079092 T>A), RS1001517204 (8:73085031 G>C)

Disease associations

OMIM: gene MIM:621005 | 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
GCST001438_7	Crohn’s disease	2.000000e-08
GCST001680_4	Corneal curvature	5.000000e-06
GCST003501_9	Asparaginase-induced acute pancreatitis in acute lymphoblastic leukemia (onset time)	2.000000e-06
GCST011828_2	Telomere length	9.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004345	corneal topography
EFO:1001507	asparaginase-induced acute pancreatitis

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	4
bisphenol A	increases methylation, increases expression, affects methylation, affects cotreatment	2
aristolochic acid I	increases expression	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression, decreases expression	1
beta-lapachone	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases expression	1
4-nonylphenol	affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-tert-octylphenol	affects cotreatment, decreases expression	1
entinostat	increases expression	1
bazedoxifene	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Coal	increases abundance, increases expression	1
Cytarabine	decreases expression	1
Dexamethasone	affects cotreatment, increases expression, decreases expression	1
Estradiol	increases expression	1
Indomethacin	affects cotreatment, increases expression, decreases expression	1
Methotrexate	increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	increases abundance, increases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Theophylline	decreases expression	1
Tretinoin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression, decreases expression	1
Cyclosporine	decreases expression	1

Clinical trials (associated diseases)

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