SPON1

Summary

SPON1 (spondin 1, HGNC:11252) is a protein-coding gene on chromosome 11p15.2, encoding Spondin-1 (Q9HCB6). Cell adhesion protein that promotes the attachment of spinal cord and sensory neuron cells and the outgrowth of neurites in vitro.

Predicted to enable LBD domain binding activity and metal ion binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be involved in cell adhesion. Predicted to act upstream of or within negative regulation of amyloid-beta formation; positive regulation of amyloid precursor protein catabolic process; and positive regulation of protein processing. Located in collagen-containing extracellular matrix and extracellular space.

Source: NCBI Gene 10418 — RefSeq curated summary.

At a glance

• GWAS associations: 28
• Clinical variants (ClinVar): 86 total
• MANE Select transcript: NM_006108

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11252
Approved symbol	SPON1
Name	spondin 1
Location	11p15.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0762, f-spondin
Ensembl gene	ENSG00000262655
Ensembl biotype	protein_coding
OMIM	604989
Entrez	10418

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000576479, ENST00000591785, ENST00000883677, ENST00000883678, ENST00000964987

RefSeq mRNA: 1 — MANE Select: NM_006108 NM_006108

CCDS: CCDS73262

Canonical transcript exons

ENST00000576479 — 16 exons

Exon	Start	End
ENSE00002637944	14243332	14243396
ENSE00002638217	13962723	13963142
ENSE00002642434	14262712	14262975
ENSE00002651197	14260588	14260752
ENSE00002656481	14075345	14075418
ENSE00002658377	14259280	14259450
ENSE00002658601	14255647	14255787
ENSE00002659545	14257716	14257898
ENSE00002664011	14041521	14041654
ENSE00002664033	14265524	14268133
ENSE00002664201	14135420	14135568
ENSE00002673403	14259534	14259701
ENSE00002673696	14079899	14080021
ENSE00002675489	13982847	13982953
ENSE00002676536	14256617	14256692
ENSE00002681017	14254528	14254729

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 98.15.

FANTOM5 (CAGE): breadth broad, TPM avg 11.1934 / max 343.7386, expressed in 642 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113189	10.3257	634
113192	0.5276	233
113188	0.3058	153
113187	0.0343	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gall bladder	UBERON:0002110	98.15	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.95	gold quality
pericardium	UBERON:0002407	97.32	gold quality
cardia of stomach	UBERON:0001162	97.24	gold quality
lower lobe of lung	UBERON:0008949	97.24	gold quality
colonic mucosa	UBERON:0000317	97.21	gold quality
mucosa of urinary bladder	UBERON:0001259	97.19	gold quality
lateral globus pallidus	UBERON:0002476	96.66	gold quality
right lung	UBERON:0002167	96.23	gold quality
visceral pleura	UBERON:0002401	95.73	gold quality
pleura	UBERON:0000977	95.25	gold quality
parietal pleura	UBERON:0002400	95.11	gold quality
jejunal mucosa	UBERON:0000399	94.97	gold quality
urinary bladder	UBERON:0001255	94.93	gold quality
rectum	UBERON:0001052	94.84	gold quality
upper lobe of lung	UBERON:0008948	94.46	gold quality
upper lobe of left lung	UBERON:0008952	94.31	gold quality
pylorus	UBERON:0001166	94.21	gold quality
endometrium	UBERON:0001295	93.99	gold quality
adult organism	UBERON:0007023	93.97	gold quality
duodenum	UBERON:0002114	93.95	gold quality
mucosa of stomach	UBERON:0001199	93.66	gold quality
lung	UBERON:0002048	93.56	gold quality
skin of hip	UBERON:0001554	93.25	gold quality
cardiac muscle of right atrium	UBERON:0003379	93.16	gold quality
germinal epithelium of ovary	UBERON:0001304	93.10	gold quality
ventral tegmental area	UBERON:0002691	91.88	gold quality
superficial temporal artery	UBERON:0001614	91.71	gold quality
smooth muscle tissue	UBERON:0001135	91.64	gold quality
fundus of stomach	UBERON:0001160	91.56	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-56	yes	1649.09
E-MTAB-8559	yes	394.92
E-HCAD-25	yes	22.01
E-GEOD-93593	yes	17.39
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FEZF2, IRX1, YBX1

miRNA regulators (miRDB)

92 targeting SPON1, 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
MMU-MIR-7116-3P	100.00	84.42	7037
MMU-MIR-6951-3P	100.00	83.23	6785
MMU-MIR-493-5P	100.00	71.77	1465
MMU-MIR-7661-5P	100.00	72.88	2389
MMU-MIR-12183-5P	100.00	69.36	1096
MMU-MIR-1903	100.00	69.30	1116
MMU-MIR-467A-3P	100.00	76.26	2736
MMU-MIR-669B-3P	100.00	76.33	2744
MMU-MIR-669F-3P	100.00	76.26	2734
MMU-MIR-297A-3P	100.00	74.21	2411
MMU-MIR-297B-3P	100.00	74.21	2411
MMU-MIR-297C-3P	100.00	74.21	2411
MMU-MIR-466A-3P	100.00	74.21	2372
MMU-MIR-466D-3P	100.00	74.21	2372
MMU-MIR-466E-3P	100.00	74.21	2372
MMU-MIR-467G	100.00	74.28	2396
MMU-MIR-669D-3P	100.00	74.21	2350
MMU-MIR-466L-3P	100.00	77.80	4451
MMU-MIR-7065-3P	100.00	72.07	2129
MMU-MIR-669H-3P	99.93	70.84	972
MMU-MIR-669K-3P	99.93	70.97	956
MMU-MIR-30F	99.92	72.08	2085
MMU-MIR-448-3P	99.90	72.68	1205
MMU-MIR-383-3P	99.90	68.92	1663
MMU-MIR-497A-3P	99.84	68.46	1114
MMU-MIR-3109-5P	99.82	67.66	411
MMU-MIR-20A-3P	99.76	69.46	775
MMU-MIR-6976-5P	99.68	66.79	1139
MMU-MIR-499-5P	99.67	70.73	780
MMU-MIR-19B-1-5P	99.65	69.52	989

Literature-anchored findings (GeneRIF, showing 17)

• expression profile of VSGP/F-spondin identifies this molecule as a potential diagnostic marker or target for developing therapeutic strategies to treat ovarian carcinoma (PMID:16103746)
• identified F-spondin as a promoting factor for cementoblastic differentiation (PMID:16965763)
• The crystal structure of the reelin-N domain resolved to 2.0 A reveals a variant immunoglobulin-like fold and potential heparin-binding sites. (PMID:18602404)
• These studies identify F-spondin as a novel protein in osteoarthritis cartilage, where it may act in situ at lesional areas to activate latent TGF-beta and induce cartilage degradation. (PMID:18780763)
• downregulates osteoclast recruitment to the root side of periodontal tissue via low-density lipoprotein receptor-related protein 8 and inhibits differentiation of osteoclastic precursors (PMID:21488757)
• The unique feature of F-spondin FS domain is the presence of three disulfide bonds associated with the N- and C-termini of the domain and a highly conserved N-linked glycosylation site. (PMID:21569239)
• These findings indicate that F-spondin regulates the differentiation of human cementoblast-like cells via BMP7 expression. (PMID:22244873)
• Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity (PMID:23471985)
• These data suggest that SPON1 may be associated with the differential rate of cognitive decline in Alzheimer disease. (PMID:23535033)
• High SPON1 expression is associated with high-grade gliomas. (PMID:24158112)
• SPON1 promotes metastatic progression through Fak and Src dependent pathway in human osteosarcoma. (PMID:26032498)
• gene expression experiment revealed that CYP2B6, SPON1, and GSG1L can be activated concomitantly through a constitutive androstane receptor (CAR) activation pathway (PMID:27010727)
• SPON1 rs2618516 polymorphism moderated the effects of APOE on working memory in terms of both in behaviors and in the level of brain activations. (PMID:29573041)
• Prognostic and Diagnostic Values of miR-506 and SPON 1 in Colorectal Cancer with Clinicopathological Considerations. (PMID:31927744)
• Evaluation of relationship between SPON1 gene and genetic susceptibility of postmenopausal osteoporosis. (PMID:32484721)
• Increased SPON1 promotes pancreatic ductal adenocarcinoma progression by enhancing IL-6 trans-signalling. (PMID:35487760)
• SPON1 is an independent prognostic biomarker for ovarian cancer. (PMID:37179355)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	spon1a	ENSDARG00000010029
mus_musculus	Spon1	ENSMUSG00000038156
rattus_norvegicus	Spon1	ENSRNOG00000058003
drosophila_melanogaster	CG17739	FBGN0033710
drosophila_melanogaster	CG30046	FBGN0050046
drosophila_melanogaster	CG30203	FBGN0050203
caenorhabditis_elegans		WBGENE00006893

Paralogs (3): THSD7A (ENSG00000005108), THSD7B (ENSG00000144229), SPON2 (ENSG00000159674)

Protein

Protein identifiers

Spondin-1 — Q9HCB6 (reviewed: Q9HCB6)

Alternative names: F-spondin, Vascular smooth muscle cell growth-promoting factor

All UniProt accessions (1): Q9HCB6

UniProt curated annotations — full annotation on UniProt →

Function. Cell adhesion protein that promotes the attachment of spinal cord and sensory neuron cells and the outgrowth of neurites in vitro. May contribute to the growth and guidance of axons in both the spinal cord and the PNS. Major factor for vascular smooth muscle cell.

Subunit / interactions. Binds to the central extracellular domain of APP and inhibits beta-secretase cleavage of APP.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Highest expression in lung, lower expression in brain, heart, kidney, liver and testis, and lowest expression in pancreas, skeletal muscle and ovary. Not expressed in spleen.

RefSeq proteins (1): NP_006099* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000884	TSP1_rpt	Repeat
IPR002861	Reeler_dom	Domain
IPR009465	Spondin_N	Domain
IPR036383	TSP1_rpt_sf	Homologous_superfamily
IPR038678	Spondin_N_sf	Homologous_superfamily
IPR042307	Reeler_sf	Homologous_superfamily
IPR044004	TSP1_spondin_dom	Domain
IPR051418	Spondin/Thrombospondin_T1	Family

Pfam: PF00090, PF02014, PF06468, PF19028

UniProt features (79 total): strand 23, disulfide bond 17, glycosylation site 10, domain 8, sequence conflict 6, turn 6, helix 4, binding site 3, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
2ZOU	X-RAY DIFFRACTION	1.45
3Q13	X-RAY DIFFRACTION	1.95
3COO	X-RAY DIFFRACTION	2
2ZOT	X-RAY DIFFRACTION	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HCB6-F1	77.62	0.31

Functional residue map

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

Ligand- & substrate-binding residues (3): 325; 354; 358

Disulfide bonds (17): 44–128, 156–182, 199–336, 200–340, 202–415, 443–480, 454–489, 459–494, 502–538, 513–517, 548–554, 559–595, 570–574, 605–610, 615–650, 626–630, 660–665

Glycosylation sites (10): 214, 448, 451, 507, 510, 564, 620, 623, 674, 681

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: 0 (showing top):

GO Biological Process (5): cell adhesion (GO:0007155), positive regulation of protein processing (GO:0010954), protein processing (GO:0016485), negative regulation of amyloid-beta formation (GO:1902430), positive regulation of amyloid precursor protein catabolic process (GO:1902993)

GO Molecular Function (4): extracellular matrix structural constituent (GO:0005201), metal ion binding (GO:0046872), LBD domain binding (GO:0050693), protein binding (GO:0005515)

GO Cellular Component (4): obsolete extracellular space (GO:0005615), endoplasmic reticulum lumen (GO:0005788), 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
cellular process	1
protein processing	1
positive regulation of proteolysis	1
regulation of protein processing	1
positive regulation of protein maturation	1
proteolysis	1
protein maturation	1
amyloid-beta formation	1
regulation of amyloid-beta formation	1
negative regulation of amyloid precursor protein catabolic process	1
amyloid precursor protein catabolic process	1
positive regulation of protein metabolic process	1
regulation of amyloid precursor protein catabolic process	1
structural molecule activity	1
extracellular matrix	1
cation binding	1
protein domain specific binding	1
binding	1
endoplasmic reticulum	1
intracellular organelle lumen	1
external encapsulating structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1296 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPON1	APP	P05067	980
SPON1	LRP8	Q14114	910
SPON1	B3GLCT	Q6Y288	811
SPON1	APBB1	O00213	781
SPON1	VLDLR	P98155	666
SPON1	POFUT2	Q9Y2G5	647
SPON1	APLP1	P51693	605
SPON1	APLP2	Q06481	604
SPON1	BACE1	P56817	592
SPON1	APOE	P02649	572
SPON1	TPX2	Q9ULW0	564
SPON1	SORL1	Q92673	554
SPON1	RSPO1	Q2MKA7	516
SPON1	GDF15	P78360	511
SPON1	SPP1	P10451	507

IntAct

24 interactions, top by confidence:

A	B	Type	Score
MEOX2	SPON1	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	SPON1	psi-mi:“MI:0915”(physical association)	0.560
MDFI	SPON1	psi-mi:“MI:0915”(physical association)	0.560
APP	SPON1	psi-mi:“MI:0915”(physical association)	0.400
SPON1	APP	psi-mi:“MI:0915”(physical association)	0.400
SPON1	APLP1	psi-mi:“MI:0915”(physical association)	0.400
APLP2	SPON1	psi-mi:“MI:0915”(physical association)	0.400
	SPON1	psi-mi:“MI:0915”(physical association)	0.370
ST14	LIPT2	psi-mi:“MI:0914”(association)	0.350
SULF2	CCDC85C	psi-mi:“MI:0914”(association)	0.350
SLURP1	MANBA	psi-mi:“MI:0914”(association)	0.350
TMPRSS13	TOR1A	psi-mi:“MI:0914”(association)	0.350
SPON1	AHCYL1	psi-mi:“MI:0914”(association)	0.350
SPON1	ARMC8	psi-mi:“MI:0914”(association)	0.350
SULF2	HNRNPCL1	psi-mi:“MI:0914”(association)	0.350
SULF2	IGHA1	psi-mi:“MI:0914”(association)	0.350
SPON1	MEOX2	psi-mi:“MI:0915”(physical association)	0.000
SPON1	MDFI	psi-mi:“MI:0915”(physical association)	0.000
SPON1	CYSRT1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (28): SPON1 (Two-hybrid), SPON1 (Two-hybrid), SPON1 (Two-hybrid), RANBP9 (Affinity Capture-MS), ARMC8 (Affinity Capture-MS), DPY19L3 (Affinity Capture-MS), SPON1 (Affinity Capture-MS), ZMYND19 (Affinity Capture-MS), GID4 (Affinity Capture-MS), C5orf22 (Affinity Capture-MS), MAEA (Affinity Capture-MS), NEDD8-MDP1 (Affinity Capture-MS), GID8 (Affinity Capture-MS), WDR26 (Affinity Capture-MS), SPON1 (Affinity Capture-MS)

ESM2 similar proteins: A0A6I8RMG7, A5A6L1, A7E2Z9, B3F211, O00622, O54775, O95388, P0C5H9, P12025, P18406, P19336, P21741, P24052, P24593, P24594, P35446, P35447, P48530, P48531, P48532, P48533, P55145, P80513, Q05717, Q07079, Q28985, Q2MKA7, Q49AH0, Q4V7M2, Q5M7L6, Q5UE90, Q5XH36, Q6DDW2, Q6DHR0, Q6P8F3, Q6UXX9, Q8BFU0, Q8R553, Q8VCC9, Q8VDA1

Diamond homologs: A0A1B0GV85, A2VE04, A4QP81, B1AXV0, D3ZE85, P0C963, P35446, P35447, Q5MGQ0, Q6INU7, Q6ZNA5, Q8K385, Q8VCC9, Q9GLX9, Q9HCB6, Q9P0K9, Q9V3Y3, Q9W770, A7MBS7, A8WGB1, B3EWY9, B3EWZ3, B3EWZ8, C0HL12, C5IAW9, D3YXG0, D3ZTD8, F1LW30, G5ECS8, O08721, O08722, O08747, O14514, O15072, O60241, O60242, O95185, O95450, P07996, P10643

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
IRX1	“up-regulates quantity by expression”	SPON1	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3716 predictions. Top by Δscore:

Variant	Effect	Δscore
11:13982845:A:AG	acceptor_gain	1.0000
11:13982846:G:GC	acceptor_gain	1.0000
11:13982846:GT:G	acceptor_gain	1.0000
11:13982846:GTA:G	acceptor_gain	1.0000
11:13982846:GTAA:G	acceptor_gain	1.0000
11:13982846:GTAAC:G	acceptor_gain	1.0000
11:13982949:TCCAG:T	donor_loss	1.0000
11:13982950:CCAG:C	donor_loss	1.0000
11:13982951:CAGG:C	donor_loss	1.0000
11:13982954:GTAAG:G	donor_loss	1.0000
11:13982955:T:A	donor_loss	1.0000
11:14041506:ACT:A	acceptor_gain	1.0000
11:14041508:T:TA	acceptor_gain	1.0000
11:14041509:G:A	acceptor_gain	1.0000
11:14041517:GTA:G	acceptor_loss	1.0000
11:14041650:CTGAA:C	donor_gain	1.0000
11:14041651:TGAA:T	donor_gain	1.0000
11:14041651:TGAAG:T	donor_loss	1.0000
11:14041652:GAA:G	donor_gain	1.0000
11:14041652:GAAG:G	donor_gain	1.0000
11:14041652:GAAGT:G	donor_loss	1.0000
11:14041653:AA:A	donor_gain	1.0000
11:14041653:AAGT:A	donor_loss	1.0000
11:14041654:AGT:A	donor_loss	1.0000
11:14041655:GTAA:G	donor_gain	1.0000
11:14041656:TAA:T	donor_loss	1.0000
11:14075416:AAGG:A	donor_loss	1.0000
11:14075418:GGTAA:G	donor_loss	1.0000
11:14075420:T:A	donor_loss	1.0000
11:14079893:TTTCA:T	acceptor_loss	1.0000

AlphaMissense

5319 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:13982885:T:C	F93L	1.000
11:13982887:C:A	F93L	1.000
11:13982887:C:G	F93L	1.000
11:14041557:T:A	C128S	1.000
11:14041557:T:C	C128R	1.000
11:14041558:G:C	C128S	1.000
11:14041570:T:A	V132D	1.000
11:14041614:T:A	W147R	1.000
11:14041614:T:C	W147R	1.000
11:14041616:G:C	W147C	1.000
11:14041616:G:T	W147C	1.000
11:14079942:C:G	C199W	1.000
11:14079959:C:A	A205D	1.000
11:14079964:T:G	Y207D	1.000
11:14079988:T:A	W215R	1.000
11:14079988:T:C	W215R	1.000
11:14079990:G:C	W215C	1.000
11:14079990:G:T	W215C	1.000
11:14135434:T:A	W231R	1.000
11:14135434:T:C	W231R	1.000
11:14135450:G:A	G236E	1.000
11:14243373:G:C	W289C	1.000
11:14243373:G:T	W289C	1.000
11:14254551:T:C	F305S	1.000
11:14254604:A:C	S323R	1.000
11:14254606:T:A	S323R	1.000
11:14254606:T:G	S323R	1.000
11:14254613:T:A	W326R	1.000
11:14254613:T:C	W326R	1.000
11:14254615:G:C	W326C	1.000

dbSNP variants (sampled 300 via entrez): RS1000002516 (11:14007656 A>G), RS1000004728 (11:14138992 A>G), RS1000041105 (11:14188281 G>T), RS1000042459 (11:13963272 C>A), RS1000045510 (11:14227844 A>G), RS1000099494 (11:14126515 C>A,T), RS1000137363 (11:14044418 C>T), RS1000167456 (11:13961079 T>A,G), RS1000201287 (11:14182055 A>G), RS1000223675 (11:13998289 A>G), RS1000226300 (11:14092706 C>A), RS1000247789 (11:14050670 G>C,T), RS1000288546 (11:13995830 A>G), RS1000288636 (11:14218621 G>A), RS1000316451 (11:14182224 C>A)

Disease associations

OMIM: gene MIM:604989 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

28 associations (top):

Study	Trait	p-value
GCST001371_10	Inflammatory biomarkers	1.000000e-06
GCST001889_1	Brain connectivity	6.000000e-10
GCST001915_26	Alzheimer’s disease (cognitive decline)	7.000000e-11
GCST002198_16	Tuberculosis	9.000000e-06
GCST003174_19	Sense of smell	7.000000e-06
GCST004824_6	P wave terminal force	2.000000e-08
GCST005162_1	Glucagon levels in response to oral glucose tolerance test (fasting)	8.000000e-07
GCST005182_13	Common carotid intima-media thickness in HIV negative individuals	5.000000e-06
GCST006143_18	Bone mineral density (total hip)	5.000000e-08
GCST006585_1077	Blood protein levels	2.000000e-13
GCST006585_1305	Blood protein levels	7.000000e-18
GCST006606_6	Response to TNF inhibitor in rheumatoid arthritis (change in swollen 28-joint count)	2.000000e-08
GCST006609_7	Response to TNF inhibitor in rheumatoid arthritis (change in tender 28-joint count)	7.000000e-06
GCST009066_23	Mosaic loss of chromosome Y (Y chromosome dosage)	2.000000e-08
GCST009391_385	Metabolite levels	4.000000e-06
GCST009731_68	Blood protein levels in cardiovascular risk	8.000000e-34
GCST010002_231	Refractive error	3.000000e-11
GCST012227_660	Hip circumference adjusted for BMI	2.000000e-09
GCST90020025_1192	Waist-to-hip ratio adjusted for BMI	3.000000e-08
GCST90020025_1193	Waist-to-hip ratio adjusted for BMI	4.000000e-08
GCST90020025_1194	Waist-to-hip ratio adjusted for BMI	2.000000e-12
GCST90020026_783	Hip index	7.000000e-12
GCST90020027_1444	Waist-hip index	8.000000e-12
GCST90020028_1823	Hip circumference adjusted for BMI	1.000000e-08
GCST90020028_1825	Hip circumference adjusted for BMI	2.000000e-09
GCST90020028_1826	Hip circumference adjusted for BMI	1.000000e-17
GCST90020028_1828	Hip circumference adjusted for BMI	2.000000e-08
GCST90020028_1829	Hip circumference adjusted for BMI	1.000000e-10

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0008379	P wave terminal force measurement
EFO:0004307	glucose tolerance test
EFO:0008463	glucagon measurement
EFO:0007702	hip bone mineral density
EFO:0004653	response to TNF antagonist
EFO:0005413	joint damage measurement
EFO:0007783	mosaic loss of chromosome Y measurement
EFO:0010437	triacylglycerol 58:10 measurement
EFO:0008290	spondin-1 measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs7104613	SPON1		0.00	0
rs77149876	SPON1		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases methylation	6
Doxorubicin	affects expression, decreases expression	3
Aflatoxin B1	decreases expression, decreases methylation, increases methylation	3
trichostatin A	affects cotreatment, decreases expression	2
sodium arsenite	affects methylation, increases expression	2
mercuric bromide	affects cotreatment, decreases expression	2
entinostat	decreases expression, increases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation	2
Estradiol	increases expression, decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
sotorasib	affects cotreatment, decreases expression	1
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
chloroquine diphosphate	increases expression	1
4-nitroso-N-phenylaniline	affects response to substance	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
triadimefon	increases expression	1
perfluorodecanoic acid	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
perfluorohexanesulfonic acid	decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
licochalcone B	increases expression	1

Clinical trials (associated diseases)

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