OMD

Summary

OMD (osteomodulin, HGNC:8134) is a protein-coding gene on chromosome 9q22.31, encoding Osteomodulin (Q99983). May be implicated in biomineralization processes.

Predicted to be involved in cell adhesion. Located in extracellular exosome.

Source: NCBI Gene 4958 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_005014

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8134
Approved symbol	OMD
Name	osteomodulin
Location	9q22.31
Locus type	gene with protein product
Status	Approved
Aliases	osteoadherin, SLRR2C
Ensembl gene	ENSG00000127083
Ensembl biotype	protein_coding
OMIM	618926
Entrez	4958

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000375550, ENST00000949678

RefSeq mRNA: 1 — MANE Select: NM_005014 NM_005014

CCDS: CCDS6696

Canonical transcript exons

ENST00000375550 — 3 exons

Exon	Start	End
ENSE00001467420	92412380	92415477
ENSE00001467421	92416619	92417574
ENSE00001467422	92424202	92424471

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 99.44.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9506 / max 314.2715, expressed in 314 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
101424	1.1410	214
101426	0.6028	181
101425	0.2068	105

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
periodontal ligament	UBERON:0008266	99.44	gold quality
right coronary artery	UBERON:0001625	97.21	gold quality
thoracic aorta	UBERON:0001515	95.99	gold quality
ascending aorta	UBERON:0001496	95.89	gold quality
descending thoracic aorta	UBERON:0002345	95.75	gold quality
tibia	UBERON:0000979	95.46	gold quality
calcaneal tendon	UBERON:0003701	94.03	gold quality
left coronary artery	UBERON:0001626	93.37	gold quality
decidua	UBERON:0002450	93.06	gold quality
coronary artery	UBERON:0001621	92.73	gold quality
aorta	UBERON:0000947	92.16	gold quality
popliteal artery	UBERON:0002250	89.44	gold quality
tibial artery	UBERON:0007610	89.40	gold quality
tendon	UBERON:0000043	88.35	gold quality
tendon of biceps brachii	UBERON:0008188	88.14	gold quality
tibial nerve	UBERON:0001323	87.82	gold quality
vena cava	UBERON:0004087	87.39	gold quality
skin of hip	UBERON:0001554	86.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.35	gold quality
mucosa of stomach	UBERON:0001199	85.68	gold quality
right atrium auricular region	UBERON:0006631	85.64	gold quality
cardiac atrium	UBERON:0002081	85.48	gold quality
cardiac muscle of right atrium	UBERON:0003379	84.81	gold quality
gall bladder	UBERON:0002110	84.47	gold quality
blood vessel layer	UBERON:0004797	83.64	gold quality
left ovary	UBERON:0002119	82.72	gold quality
omental fat pad	UBERON:0010414	82.58	gold quality
peritoneum	UBERON:0002358	82.56	gold quality
upper leg skin	UBERON:0004262	82.43	gold quality
right ovary	UBERON:0002118	82.22	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	395.75
E-ANND-3	yes	20.67
E-CURD-112	yes	17.09

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): BMP2, CNBP, TCF3, TGFB1

miRNA regulators (miRDB)

48 targeting OMD, 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-656-3P	100.00	72.15	2788
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-106A-3P	99.53	67.58	995
HSA-MIR-7159-3P	99.51	70.17	1920
HSA-MIR-302B-5P	99.50	69.49	1857
HSA-MIR-302D-5P	99.50	69.34	1863
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-12132	99.47	68.90	1341
HSA-MIR-4735-5P	99.43	68.49	1780
HSA-MIR-1276	99.36	68.18	1642

Literature-anchored findings (GeneRIF, showing 7)

• TGF beta 1 signaling and stimulation of osteoadherin in human pulpal fibroblasts and in early secretory and mature odontoblasts (PMID:12489179)
• tyrosine sulfate-rich domains of the LRR proteins fibromodulin and osteoadherin bind motifs of basic clusters in a variety of heparin-binding proteins, including bioactive factors (PMID:19700767)
• Osteomodulin, osteoglycin, and asporin appear to be distinctly regulated in osteoarthritis labrum compared to OA cartilage. (PMID:25371314)
• Osteomodulin (OMD) directly binds to type 1 collagen. OMD suppresses formation of collagen fibrils. (PMID:26003732)
• Osteomodulin is a Potential Genetic Target for Hypertrophic Cardiomyopathy. (PMID:33715137)
• Osteomodulin Gene Expression Is Associated With Plaque Calcification, Stability, and Fewer Cardiovascular Events in the CPIP Cohort. (PMID:35135320)
• Osteomodulin contributes to keloid development by regulating p38 MAPK signaling. (PMID:37017425)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	omd	ENSDARG00000093600
mus_musculus	Omd	ENSMUSG00000048368
rattus_norvegicus	Omd	ENSRNOG00000039560

Paralogs (10): EPYC (ENSG00000083782), OGN (ENSG00000106809), ECM2 (ENSG00000106823), FMOD (ENSG00000122176), OMG (ENSG00000126861), LUM (ENSG00000139329), KERA (ENSG00000139330), PRELP (ENSG00000188783), LINGO4 (ENSG00000213171), LINGO3 (ENSG00000220008)

Protein

Protein identifiers

Osteomodulin — Q99983 (reviewed: Q99983)

Alternative names: Keratan sulfate proteoglycan osteomodulin, Osteoadherin

All UniProt accessions (1): Q99983

UniProt curated annotations — full annotation on UniProt →

Function. May be implicated in biomineralization processes. Has a function in binding of osteoblasts via the alpha(V)beta(3)-integrin.

Subunit / interactions. Binds the alpha(V)beta(3)-integrin.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Bone specific.

Post-translational modifications. Glycosylated; contains keratan sulfate.

Similarity. Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.

RefSeq proteins (1): NP_005005* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000372	LRRNT	Domain
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050333	SLRP	Family

Pfam: PF13855

UniProt features (60 total): strand 13, repeat 11, modified residue 9, helix 6, glycosylation site 5, sequence variant 5, turn 4, compositionally biased region 2, signal peptide 1, chain 1, region of interest 1, domain 1, disulfide bond 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
5YQ5	X-RAY DIFFRACTION	2.17

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99983-F1	81.82	0.71

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 (9): 22, 25, 31, 39, 51, 58, 77, 416, 417

Disulfide bonds (1): 321–353

Glycosylation sites (5): 113, 121, 187, 242, 316

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-2022854	Keratan sulfate biosynthesis
R-HSA-2022857	Keratan sulfate degradation
R-HSA-3656225	Defective CHST6 causes MCDC1
R-HSA-3656243	Defective ST3GAL3 causes MCT12 and EIEE15
R-HSA-3656244	Defective B4GALT1 causes B4GALT1-CDG (CDG-2d)

MSigDB gene sets: 142 (showing top): BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP, YAGI_AML_WITH_INV_16_TRANSLOCATION, XU_GH1_AUTOCRINE_TARGETS_UP, CEBP_Q2, MCLACHLAN_DENTAL_CARIES_DN, BOQUEST_STEM_CELL_CULTURED_VS_FRESH_DN, INGRAM_SHH_TARGETS_UP, MODULE_99, HFH3_01, TGANTCA_AP1_C, BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN, HFH1_01, BROWNE_HCMV_INFECTION_6HR_UP, chr9q22, GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP

GO Biological Process (1): cell adhesion (GO:0007155)

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

GO Cellular Component (6): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), Golgi lumen (GO:0005796), extracellular matrix (GO:0031012), lysosomal lumen (GO:0043202), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Diseases associated with glycosaminoglycan metabolism	3
Keratan sulfate/keratin metabolism	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular process	1
binding	1
cellular anatomical structure	1
Golgi apparatus	1
intracellular organelle lumen	1
external encapsulating structure	1
lysosome	1
vacuolar lumen	1
extracellular vesicle	1

Protein interactions and networks

STRING

1208 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OMD	SPARC	P09486	634
OMD	OGN	P20774	634
OMD	ASPN	Q9BXN1	601
OMD	C4A	P01028	570
OMD	C4A	P01028	568
OMD	CHAD	O15335	559
OMD	DMP1	Q13316	530
OMD	IBSP	P21815	516
OMD	MMP13	P45452	512
OMD	AHSG	P02765	506
OMD	PRELP	P51888	495
OMD	FMOD	Q06828	487
OMD	OSM	P13725	473
OMD	ACAN	P16112	441
OMD	CRP	P02741	435

IntAct

4 interactions, top by confidence:

A	B	Type	Score
OMD	SPTAN1	psi-mi:“MI:0915”(physical association)	0.400
OMD	APAF1	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): APAF1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), BBS1 (Affinity Capture-MS), SUMF1 (Affinity Capture-MS), OMD (Proximity Label-MS), BBS1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), APAF1 (Affinity Capture-MS)

ESM2 similar proteins: C0STK7, G5EFX6, G5EG78, O15455, O35103, O35367, O42235, O60938, O62702, O73798, O75094, O77742, O88280, O94813, P08953, P24014, P24348, P46023, Q04833, Q0PV50, Q3ZBN5, Q58A48, Q5RI43, Q5TJ59, Q65YW8, Q65Z91, Q6AXL3, Q6R5N8, Q6X0I2, Q8C031, Q8SXT3, Q965M2, Q99983, Q99MB1, Q99MQ4, Q9BXN1, Q9CQ76, Q9DE66, Q9HCJ2, Q9JI18

Diamond homologs: O35103, O35367, O42235, O46378, O46379, O60938, O62702, O75093, O77742, P07585, P13605, P21793, P28675, P50608, P50609, P51884, P51885, P51886, P51887, P51888, P51890, P58681, P58874, P83286, Q05443, Q06828, Q5R1V9, Q5RI43, Q6GLE8, Q7Z5L7, Q99983, Q99MQ4, Q9DE66, Q9DE67, Q9DE68, Q9EQP5, Q9EQU3, Q9GKN8, Q9IB75, Q9JK53

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
BMP2	“up-regulates quantity by expression”	OMD	“transcriptional regulation”
TGFB1	“down-regulates quantity by repression”	OMD	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

460 predictions. Top by Δscore:

Variant	Effect	Δscore
9:92417516:C:CT	acceptor_gain	1.0000
9:92417516:C:T	acceptor_gain	1.0000
9:92415473:CATCT:C	acceptor_gain	0.9900
9:92415475:TCT:T	acceptor_gain	0.9900
9:92415476:CT:C	acceptor_gain	0.9900
9:92415476:CTC:C	acceptor_gain	0.9900
9:92415477:TCT:T	acceptor_gain	0.9900
9:92415477:TCTGA:T	acceptor_loss	0.9900
9:92415478:C:CC	acceptor_gain	0.9900
9:92415478:C:CG	acceptor_loss	0.9900
9:92415478:C:G	acceptor_gain	0.9900
9:92415479:T:A	acceptor_loss	0.9900
9:92417517:A:T	acceptor_gain	0.9900
9:92416621:T:A	donor_gain	0.9800
9:92424196:TCATA:T	donor_loss	0.9800
9:92424197:CATAC:C	donor_loss	0.9800
9:92424198:ATAC:A	donor_loss	0.9800
9:92424199:TAC:T	donor_loss	0.9800
9:92424200:ACCTG:A	donor_loss	0.9800
9:92424201:C:CG	donor_loss	0.9800
9:92415474:ATCT:A	acceptor_gain	0.9700
9:92415480:G:C	acceptor_loss	0.9700
9:92416617:A:AC	donor_gain	0.9600
9:92416618:C:CC	donor_gain	0.9600
9:92416618:CTTT:C	donor_gain	0.9500
9:92420971:AT:A	donor_gain	0.9500
9:92415900:T:A	acceptor_gain	0.9400
9:92417574:CCTAT:C	acceptor_gain	0.9400
9:92415474:ATCTC:A	acceptor_gain	0.9300
9:92415475:TCTCT:T	acceptor_gain	0.9300

AlphaMissense

2849 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:92415411:C:G	R336P	0.996
9:92416645:A:G	L305P	0.995
9:92417194:A:G	L122P	0.995
9:92416846:A:G	L238P	0.994
9:92416705:A:G	L285P	0.993
9:92417122:A:G	L146P	0.992
9:92417266:A:G	L98P	0.992
9:92415398:A:C	N340K	0.991
9:92415398:A:T	N340K	0.991
9:92416830:A:C	N243K	0.991
9:92416830:A:T	N243K	0.991
9:92417326:C:G	C78S	0.991
9:92417327:A:T	C78S	0.991
9:92415361:A:G	C353R	0.989
9:92415456:C:G	C321S	0.989
9:92415457:A:T	C321S	0.989
9:92417326:C:T	C78Y	0.989
9:92415423:A:G	L332S	0.988
9:92415457:A:G	C321R	0.988
9:92416909:A:G	L217P	0.988
9:92415399:T:A	N340I	0.987
9:92415359:G:C	C353W	0.986
9:92416629:A:C	N310K	0.986
9:92416629:A:T	N310K	0.986
9:92416774:A:G	L262P	0.986
9:92417059:A:G	L167P	0.986
9:92417116:A:G	L148P	0.986
9:92417325:A:C	C78W	0.986
9:92416684:A:G	L292S	0.985
9:92416987:A:G	L191P	0.985

dbSNP variants (sampled 300 via entrez): RS1000286336 (9:92423808 C>T), RS1000711630 (9:92422787 A>G), RS1001184149 (9:92421568 G>A), RS1001223864 (9:92416016 A>G), RS1001320171 (9:92421953 G>A), RS1001389848 (9:92414882 A>G), RS1001838906 (9:92423338 T>C), RS1002250545 (9:92420659 A>C), RS1002322504 (9:92420344 G>C), RS1002796726 (9:92413258 A>G,T), RS1002845537 (9:92425100 G>A), RS1003007113 (9:92418678 T>C), RS1003327282 (9:92419050 C>T), RS1003469683 (9:92418366 C>A,T), RS1003525248 (9:92426446 A>T)

Disease associations

OMIM: gene MIM:618926 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST010725_16	Malaria	9.000000e-06
GCST010725_28	Malaria	6.000000e-06
GCST010725_95	Malaria	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Diethylhexyl Phthalate	decreases expression, affects cotreatment	2
Progesterone	increases expression	2
bisphenol A	affects cotreatment, increases expression	1
diisononyl phthalate	affects cotreatment, decreases expression	1
lead nitrate	affects cotreatment, decreases expression	1
butylbenzyl phthalate	affects cotreatment, decreases expression	1
triadimefon	decreases expression	1
CGP 52608	affects binding, increases reaction	1
incobotulinumtoxinA	increases expression	1
Berberine	increases expression	1
Cadmium	decreases expression, increases abundance	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Mercury	affects cotreatment, decreases expression	1
Nickel	decreases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1
Cadmium Chloride	decreases expression, increases abundance	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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