OLFML2B

Summary

OLFML2B (olfactomedin like 2B, HGNC:24558) is a protein-coding gene on chromosome 1q23.3, encoding Olfactomedin-like protein 2B (Q68BL8).

This gene encodes an olfactomedin domain-containing protein. Most olfactomedin domain-containing proteins are secreted glycoproteins.

Source: NCBI Gene 25903 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 140 total — 5 likely-pathogenic
• MANE Select transcript: NM_015441

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24558
Approved symbol	OLFML2B
Name	olfactomedin like 2B
Location	1q23.3
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP586L151
Ensembl gene	ENSG00000162745
Ensembl biotype	protein_coding
Entrez	25903

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 nonsense_mediated_decay

ENST00000294794, ENST00000367938, ENST00000367940, ENST00000525589, ENST00000533556

RefSeq mRNA: 3 — MANE Select: NM_015441 NM_001297713, NM_001347700, NM_015441

CCDS: CCDS1236, CCDS72966

Canonical transcript exons

ENST00000294794 — 8 exons

Exon	Start	End
ENSE00001068175	161997825	161998349
ENSE00001068176	161984804	161984980
ENSE00001426436	162006297	162006473
ENSE00001426945	162000113	162000338
ENSE00001427645	162019919	162020182
ENSE00001429357	162023257	162023869
ENSE00001445970	161983192	161984276
ENSE00001733402	162017400	162017507

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 96.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.2389 / max 339.4375, expressed in 1100 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15660	11.7433	1065
15658	1.2000	403
15661	0.4189	185
15659	0.3473	190
15664	0.2357	111
15662	0.1842	88
15663	0.0633	33
201792	0.0422	13
15656	0.0040	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	96.44	gold quality
periodontal ligament	UBERON:0008266	96.06	gold quality
gall bladder	UBERON:0002110	94.36	gold quality
vena cava	UBERON:0004087	93.59	gold quality
stromal cell of endometrium	CL:0002255	93.36	gold quality
right coronary artery	UBERON:0001625	93.02	gold quality
popliteal artery	UBERON:0002250	92.56	gold quality
tibial artery	UBERON:0007610	92.56	gold quality
aorta	UBERON:0000947	91.49	gold quality
saphenous vein	UBERON:0007318	90.77	gold quality
left coronary artery	UBERON:0001626	90.45	gold quality
thoracic aorta	UBERON:0001515	90.22	gold quality
ascending aorta	UBERON:0001496	90.21	gold quality
coronary artery	UBERON:0001621	89.87	gold quality
descending thoracic aorta	UBERON:0002345	89.83	gold quality
left testis	UBERON:0004533	89.14	gold quality
calcaneal tendon	UBERON:0003701	89.10	gold quality
right testis	UBERON:0004534	88.21	gold quality
tibial nerve	UBERON:0001323	88.18	gold quality
synovial joint	UBERON:0002217	88.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.05	gold quality
urethra	UBERON:0000057	88.05	gold quality
frontal pole	UBERON:0002795	87.76	silver quality
subcutaneous adipose tissue	UBERON:0002190	87.54	gold quality
skin of hip	UBERON:0001554	87.51	gold quality
testis	UBERON:0000473	87.49	gold quality
paraflocculus	UBERON:0005351	87.21	silver quality
muscle layer of sigmoid colon	UBERON:0035805	87.05	gold quality
layer of synovial tissue	UBERON:0007616	86.79	gold quality
sperm	CL:0000019	86.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	38.53
E-CURD-112	yes	15.57
E-ANND-3	yes	13.15
E-MTAB-6678	yes	10.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting OLFML2B, 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-1277-5P	100.00	73.95	5056
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-664B-3P	99.84	71.65	3590

Literature-anchored findings (GeneRIF, showing 1)

• The high expression of OLFML2B was associate with a short overall survival in gastric cancer patients. (PMID:30866865)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	olfml2ba	ENSDARG00000005716
danio_rerio	olfml2bb	ENSDARG00000021480
mus_musculus	Olfml2b	ENSMUSG00000038463
rattus_norvegicus	Olfml2b	ENSRNOG00000003018

Paralogs (9): MYOC (ENSG00000034971), OLFM4 (ENSG00000102837), OLFM2 (ENSG00000105088), OLFML3 (ENSG00000116774), OLFM3 (ENSG00000118733), OLFM1 (ENSG00000130558), OLFML1 (ENSG00000183801), OLFML2A (ENSG00000185585), GLDN (ENSG00000186417)

Protein

Protein identifiers

Olfactomedin-like protein 2B — Q68BL8 (reviewed: Q68BL8)

Alternative names: Photomedin-2

All UniProt accessions (4): Q68BL8, F2Z3N3, H0YE85, H0YEW8

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Homodimer. Binds to heparin and chondroitin sulfate E.

Subcellular location. Secreted.

Post-translational modifications. O-glycosylated and N-glycosylated.

Isoforms (2)

UniProt ID	Names	Canonical?
Q68BL8-1	1	yes
Q68BL8-2	2

RefSeq proteins (3): NP_001284642, NP_001334629, NP_056256* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003112	Olfac-like_dom	Domain
IPR050605	Olfactomedin-like_domain	Family

Pfam: PF02191

UniProt features (17 total): glycosylation site 3, compositionally biased region 3, sequence variant 2, region of interest 2, coiled-coil region 2, signal peptide 1, chain 1, disulfide bond 1, splice variant 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q68BL8-F1	63.26	0.28

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 (1): 494–680

Glycosylation sites (3): 187, 213, 695

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 138 (showing top): BENPORATH_ES_WITH_H3K27ME3, MODULE_45, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, STARK_HYPPOCAMPUS_22Q11_DELETION_UP, MODULE_118, INGRAM_SHH_TARGETS_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, POU3F2_02, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN, RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, MODULE_207, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GRYDER_PAX3FOXO1_TOP_ENHANCERS, MASSARWEH_TAMOXIFEN_RESISTANCE_UP

GO Biological Process (2): signal transduction (GO:0007165), extracellular matrix organization (GO:0030198)

GO Molecular Function (2): identical protein binding (GO:0042802), extracellular matrix binding (GO:0050840)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), extracellular matrix (GO:0031012), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
extracellular structure organization	1
external encapsulating structure organization	1
protein binding	1
binding	1
external encapsulating structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

864 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OLFML2B	NOS1AP	O75052	487
OLFML2B	TOR3A	Q9H497	447
OLFML2B	TMEM220	Q6QAJ8	435
OLFML2B	TOR1AIP1	Q5JTV8	431
OLFML2B	TDRD5	Q8NAT2	425
OLFML2B	CEP350	Q5VT06	418
OLFML2B	SEC16B	Q96JE7	408
OLFML2B	EXOSC9	Q06265	402
OLFML2B	QSOX1	O00391	398
OLFML2B	SOAT1	P35610	398
OLFML2B	RNF222	A6NCQ9	394
OLFML2B	ATF6	P18850	391
OLFML2B	C1orf94	Q6P1W5	391
OLFML2B	MXRA5	Q9NR99	375
OLFML2B	NATD1	Q8N6N6	371

IntAct

4 interactions, top by confidence:

A	B	Type	Score
OLFML2B	H2AC12	psi-mi:“MI:0915”(physical association)	0.400
OLFML2B	HSPA5	psi-mi:“MI:0914”(association)	0.350
OLFML2B	PDIA4	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): OLFML2B (Affinity Capture-RNA), HIST1H2AH (Proximity Label-MS), OLFML2B (Affinity Capture-MS), OLFML2B (Affinity Capture-RNA), ERF (Affinity Capture-MS), LONP2 (Affinity Capture-MS), DNAJC3 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), CHSY1 (Affinity Capture-MS), NEDD8 (Reconstituted Complex), OLFML2B (Affinity Capture-Western), OLFML2B (Affinity Capture-MS)

ESM2 similar proteins: A1XQX3, A1XQY0, A1XQY3, A2ALI5, A6QLD2, B5X216, D0PRN4, E9PUN2, O35181, O75151, O94933, O94991, P0C7U0, P15379, P23470, P49415, P56975, P58401, P80560, Q05909, Q3SXY7, Q3UH99, Q3V1G4, Q4W8E7, Q58EG3, Q5EGE1, Q5R3F8, Q5R5B8, Q63376, Q63475, Q68BL8, Q68FM6, Q6QD51, Q6ZSJ9, Q76KF0, Q80Z10, Q810B7, Q810B9, Q8AXP2, Q8C8T7

Diamond homologs: A2BD09, A4IIT5, A6QLD2, B0BNI5, B5MFE9, O70624, O88917, O88923, O88998, O94910, O95490, O95897, O97817, O97827, O97831, P63056, P63057, Q0P3W2, Q0V9V5, Q0VCP3, Q25C36, Q2PT31, Q3UZZ4, Q3V1G4, Q568Y7, Q594P2, Q62609, Q66H86, Q68BL7, Q68BL8, Q6UWY5, Q6UX06, Q80TR1, Q80TS3, Q863A3, Q866N2, Q8BHP7, Q8BK62, Q8BM13, Q8JZZ7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	5
Uncertain significance	117
Likely benign	5
Benign	3

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
217134	NM_015441.3(OLFML2B):c.44T>G (p.Val15Gly)	Likely pathogenic
217135	NM_015441.3(OLFML2B):c.1039C>T (p.Arg347Trp)	Likely pathogenic
217137	NM_015441.3(OLFML2B):c.1306G>T (p.Ala436Ser)	Likely pathogenic
217140	NM_015441.3(OLFML2B):c.2021G>A (p.Gly674Asp)	Likely pathogenic
217141	NM_015441.3(OLFML2B):c.1606G>A (p.Gly536Ser)	Likely pathogenic

SpliceAI

1017 predictions. Top by Δscore:

Variant	Effect	Δscore
1:161984272:GCGAC:G	acceptor_gain	1.0000
1:161984273:CGAC:C	acceptor_gain	1.0000
1:161984273:CGACC:C	acceptor_gain	1.0000
1:161984274:GAC:G	acceptor_gain	1.0000
1:161984277:C:CC	acceptor_gain	1.0000
1:161984281:A:T	acceptor_gain	1.0000
1:161984283:G:C	acceptor_gain	1.0000
1:161984283:G:GC	acceptor_gain	1.0000
1:161984799:TGTAC:T	donor_loss	1.0000
1:161984800:GTACC:G	donor_loss	1.0000
1:161984801:TA:T	donor_loss	1.0000
1:161984802:A:T	donor_loss	1.0000
1:161984977:CTTC:C	acceptor_gain	1.0000
1:161984982:T:A	acceptor_loss	1.0000
1:161998347:CTT:C	acceptor_gain	1.0000
1:161998350:C:CC	acceptor_gain	1.0000
1:162000111:A:AC	donor_gain	1.0000
1:162000112:C:CC	donor_gain	1.0000
1:162000112:CG:C	donor_gain	1.0000
1:162000112:CGCTG:C	donor_gain	1.0000
1:162000347:C:CT	acceptor_gain	1.0000
1:162000348:A:T	acceptor_gain	1.0000
1:162006296:CCT:C	donor_gain	1.0000
1:162006470:CTTC:C	acceptor_gain	1.0000
1:162006471:TTC:T	acceptor_gain	1.0000
1:162006472:TC:T	acceptor_gain	1.0000
1:162006472:TCC:T	acceptor_loss	1.0000
1:162006473:CC:C	acceptor_gain	1.0000
1:162006473:CCTG:C	acceptor_loss	1.0000
1:162006474:C:CC	acceptor_gain	1.0000

AlphaMissense

4879 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:161983722:A:G	W736R	1.000
1:161983722:A:T	W736R	1.000
1:161983889:C:T	C680Y	1.000
1:161984906:A:G	W517R	1.000
1:161984906:A:T	W517R	1.000
1:161984912:C:A	G515W	1.000
1:161983720:C:A	W736C	0.999
1:161983720:C:G	W736C	0.999
1:161983730:A:T	L733H	0.999
1:161983832:G:T	A699D	0.999
1:161983888:A:C	C680W	0.999
1:161983889:C:A	C680F	0.999
1:161983890:A:G	C680R	0.999
1:161984040:A:G	W630R	0.999
1:161984040:A:T	W630R	0.999
1:161984241:A:G	W563R	0.999
1:161984241:A:T	W563R	0.999
1:161984829:G:C	F542L	0.999
1:161984829:G:T	F542L	0.999
1:161984830:A:G	F542S	0.999
1:161984831:A:G	F542L	0.999
1:161984839:A:G	L539P	0.999
1:161984904:C:A	W517C	0.999
1:161984904:C:G	W517C	0.999
1:161984911:C:T	G515E	0.999
1:161984912:C:G	G515R	0.999
1:161984912:C:T	G515R	0.999
1:161984962:A:T	L498H	0.999
1:161984974:C:G	C494S	0.999
1:161984975:A:G	C494R	0.999

dbSNP variants (sampled 300 via entrez): RS1000026205 (1:161983372 G>A,T), RS1000087157 (1:161989797 A>G), RS1000093366 (1:162018107 A>T), RS1000158221 (1:162003884 C>A,T), RS1000244329 (1:161994744 T>A), RS1000276306 (1:162012083 T>C), RS1000383262 (1:162005749 A>G,T), RS1000501152 (1:162005629 C>T), RS1000618744 (1:162005482 T>C), RS1000700953 (1:162005693 A>C), RS1000858514 (1:162016793 A>G), RS1000941338 (1:162011058 G>A,C), RS1001109740 (1:162017033 A>T), RS1001109828 (1:162016891 A>T), RS1001127866 (1:162015238 C>G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST000444_1	QT interval	1.000000e-83
GCST001650_1	C-reactive protein	1.000000e-37
GCST001650_11	C-reactive protein	3.000000e-10
GCST001650_8	C-reactive protein	4.000000e-73
GCST003872_5	QRS complex (12-leadsum)	1.000000e-09
GCST006493_9	Systemic sclerosis	7.000000e-06
GCST011010_29	Electrocardiographic traits (multivariate)	1.000000e-11
GCST012480_6	C-reactive protein levels	4.000000e-12
GCST90002380_115	Basophil percentage of white cells	9.000000e-10

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004682	QT interval
EFO:0004458	C-reactive protein measurement
EFO:0005054	QRS complex
EFO:0007742	QRS amplitude
EFO:0004327	electrocardiography
EFO:0007992	basophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	4
Benzo(a)pyrene	increases methylation, affects methylation	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	increases expression	1
bisphenol A	affects methylation, decreases methylation, affects cotreatment	1
sodium bichromate	decreases expression	1
sulforaphane	decreases expression	1
perfluorooctanoic acid	increases expression	1
benzo(e)pyrene	increases methylation, decreases methylation	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
aflatoxin B2	increases methylation	1
nickel sulfate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
azoxystrobin	decreases expression	1
CGP 52608	increases reaction, affects binding	1
deguelin	decreases expression	1
2-palmitoylglycerol	increases expression	1
fenpyroximate	decreases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	decreases expression	1
pyrimidifen	decreases expression	1
thifluzamide	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pyrachlostrobin	decreases expression	1
incobotulinumtoxinA	increases expression	1
picoxystrobin	decreases expression	1
Fulvestrant	affects cotreatment, affects methylation	1
Azathioprine	increases expression	1
Cadmium	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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