OLFML2A

Summary

OLFML2A (olfactomedin like 2A, HGNC:27270) is a protein-coding gene on chromosome 9q33.3, encoding Olfactomedin-like protein 2A (Q68BL7).

Predicted to enable extracellular matrix binding activity and identical protein binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within extracellular matrix organization. Predicted to be located in extracellular matrix and extracellular region. Predicted to be active in extracellular space.

Source: NCBI Gene 169611 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 183 total
• MANE Select transcript: NM_182487

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27270
Approved symbol	OLFML2A
Name	olfactomedin like 2A
Location	9q33.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ00237
Ensembl gene	ENSG00000185585
Ensembl biotype	protein_coding
OMIM	615899
Entrez	169611

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000288815, ENST00000331715, ENST00000373580, ENST00000863982, ENST00000863983, ENST00000928170

RefSeq mRNA: 2 — MANE Select: NM_182487 NM_001282715, NM_182487

CCDS: CCDS65129, CCDS6857

Canonical transcript exons

ENST00000373580 — 8 exons

Exon	Start	End
ENSE00001036076	124799285	124799491
ENSE00001091369	124801414	124801663
ENSE00001214743	124786975	124787238
ENSE00001420201	124795024	124795131
ENSE00001629407	124807781	124807966
ENSE00001700932	124809808	124814882
ENSE00001737151	124777133	124777360
ENSE00002717850	124804094	124804342

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 97.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.0111 / max 164.3908, expressed in 1013 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98480	3.2897	854
98481	1.7979	557
98482	1.5305	507
98483	0.3929	224

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
dorsal root ganglion	UBERON:0000044	97.78	gold quality
trigeminal ganglion	UBERON:0001675	97.58	gold quality
mammary duct	UBERON:0001765	91.90	gold quality
skin of hip	UBERON:0001554	91.36	gold quality
epithelium of mammary gland	UBERON:0003244	90.12	gold quality
urethra	UBERON:0000057	89.61	gold quality
synovial joint	UBERON:0002217	89.41	gold quality
colonic epithelium	UBERON:0000397	89.22	gold quality
tibia	UBERON:0000979	88.61	gold quality
upper leg skin	UBERON:0004262	88.08	gold quality
thoracic mammary gland	UBERON:0005200	87.81	gold quality
mammary gland	UBERON:0001911	87.72	gold quality
left ventricle myocardium	UBERON:0006566	87.71	gold quality
penis	UBERON:0000989	87.68	gold quality
nipple	UBERON:0002030	87.59	gold quality
upper arm skin	UBERON:0004263	87.07	gold quality
muscle layer of sigmoid colon	UBERON:0035805	86.92	gold quality
sural nerve	UBERON:0015488	86.77	gold quality
stromal cell of endometrium	CL:0002255	86.60	gold quality
spleen	UBERON:0002106	86.47	gold quality
body of uterus	UBERON:0009853	86.41	gold quality
mammalian vulva	UBERON:0000997	86.39	gold quality
ectocervix	UBERON:0012249	86.22	gold quality
mucosa of stomach	UBERON:0001199	86.17	gold quality
layer of synovial tissue	UBERON:0007616	85.78	gold quality
cardiac muscle of right atrium	UBERON:0003379	85.77	gold quality
seminal vesicle	UBERON:0000998	85.64	gold quality
myometrium	UBERON:0001296	85.22	gold quality
endocervix	UBERON:0000458	85.09	gold quality
uterine cervix	UBERON:0000002	84.91	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

140 targeting OLFML2A, 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-3613-3P	100.00	76.36	7965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-130B-5P	99.83	68.50	1888

Literature-anchored findings (GeneRIF, showing 1)

• Three neuronal proteins (Huntingtin interacting protein 1, neurofascin, and olfactomedin-like 2a) are novel components of podocyte major processes and their expression in glomerular crescents supports their role in crescent formation. (PMID:22913984)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	olfml2a	ENSDARG00000005648
danio_rerio	OLFML2A	ENSDARG00000113533
mus_musculus	Olfml2a	ENSMUSG00000046618
rattus_norvegicus	Olfml2a	ENSRNOG00000014034

Paralogs (9): MYOC (ENSG00000034971), OLFM4 (ENSG00000102837), OLFM2 (ENSG00000105088), OLFML3 (ENSG00000116774), OLFM3 (ENSG00000118733), OLFM1 (ENSG00000130558), OLFML2B (ENSG00000162745), OLFML1 (ENSG00000183801), GLDN (ENSG00000186417)

Protein

Protein identifiers

Olfactomedin-like protein 2A — Q68BL7 (reviewed: Q68BL7)

Alternative names: Photomedin-1

All UniProt accessions (2): Q68BL7, Q5JTM7

UniProt curated annotations — full annotation on UniProt →

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

Subcellular location. Secreted.

Tissue specificity. In the kidney expressed only by podocytes, wherein they localize to major processes.

Post-translational modifications. May be cleaved at Lys-295 after secretion. O-glycosylated but not N-glycosylated.

Isoforms (3)

UniProt ID	Names	Canonical?
Q68BL7-1	1	yes
Q68BL7-2	2
Q68BL7-3	3

RefSeq proteins (2): NP_001269644, NP_872293* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF02191

UniProt features (19 total): compositionally biased region 6, splice variant 3, sequence variant 2, region of interest 2, signal peptide 1, chain 1, site 1, disulfide bond 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q68BL7-F1	68.33	0.33

Functional residue map

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

Catalytic / active sites (1): 294–295 (cleavage)

Disulfide bonds (1): 395–582

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 135 (showing top): WALLACE_PROSTATE_CANCER_RACE_UP, LFA1_Q6, AREB6_01, BROWNE_HCMV_INFECTION_48HR_DN, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP, TGCTGAY_UNKNOWN, HEN1_01, ACATTCC_MIR1_MIR206, ATF3_Q6, PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP, CERVERA_SDHB_TARGETS_1_UP, NERF_Q2, FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, FRASOR_RESPONSE_TO_ESTRADIOL_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

646 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OLFML2A	TCF24	Q7RTU0	506
OLFML2A	ZNF511	Q8NB15	474
OLFML2A	ANKRD29	Q8N6D5	447
OLFML2A	IPP	Q9Y573	392
OLFML2A	LYPD5	Q6UWN5	391
OLFML2A	ARAP2	Q8WZ64	388
OLFML2A	PARVG	Q9HBI0	387
OLFML2A	TOR1AIP2	Q8NFQ8	373
OLFML2A	ADGRL4	Q9HBW9	371
OLFML2A	TOR1AIP1	Q5JTV8	353
OLFML2A	TMEM47	Q9BQJ4	351
OLFML2A	NR6A1	Q15406	351
OLFML2A	LDB2	O43679	344
OLFML2A	ZC4H2	Q9NQZ6	341
OLFML2A	NALF2	O75949	339
OLFML2A	LMNTD2	Q8IXW0	339

IntAct

8 interactions, top by confidence:

A	B	Type	Score
IL5RA	POTEF	psi-mi:“MI:0914”(association)	0.350
ADIPOQ	PLOD2	psi-mi:“MI:0914”(association)	0.350
ADIPOQ	AGRN	psi-mi:“MI:0914”(association)	0.350
CLGN	TMEM131L	psi-mi:“MI:0914”(association)	0.350
OLFM2	CLGN	psi-mi:“MI:0914”(association)	0.350
OLFML2B	PDIA4	psi-mi:“MI:0914”(association)	0.350
	MANBA	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (11): OLFML2A (Reconstituted Complex), OLFML2A (Biochemical Activity), OLFML2A (Affinity Capture-RNA), OLFML2A (Proximity Label-MS), OLFML2A (Proximity Label-MS), OLFML2A (Affinity Capture-RNA), OLFML2A (Affinity Capture-MS), OLFML2A (Affinity Capture-MS), OLFML2A (Proximity Label-MS), OLFML2A (Cross-Linking-MS (XL-MS)), APP (Reconstituted Complex)

ESM2 similar proteins: A2A699, A2BD09, A4IIT5, A5D7T4, A6QLD2, A8MVW0, O35764, O43278, O70624, O95502, O95897, P35054, P51693, Q03157, Q2PT31, Q3UPI1, Q3UZZ4, Q3V1G4, Q568Y7, Q594P2, Q5QQ37, Q66H86, Q68BL7, Q68BL8, Q6AYE5, Q6P7B4, Q6UWH4, Q6UWY5, Q6ZMI3, Q701R2, Q701R3, Q701R4, Q766D5, Q76KP1, Q80WL1, Q863A3, Q866N2, Q86VZ4, Q8BHP7, Q8BM13

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	162
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1409 predictions. Top by Δscore:

Variant	Effect	Δscore
9:124777356:GTAAG:G	donor_gain	1.0000
9:124777360:GGTA:G	donor_loss	1.0000
9:124795018:G:A	acceptor_gain	1.0000
9:124795022:A:AG	acceptor_gain	1.0000
9:124795023:G:GA	acceptor_gain	1.0000
9:124795023:GCT:G	acceptor_gain	1.0000
9:124795129:GAG:G	donor_gain	1.0000
9:124795132:G:GC	donor_loss	1.0000
9:124795133:T:A	donor_loss	1.0000
9:124800776:A:G	donor_gain	1.0000
9:124801410:CCA:C	acceptor_loss	1.0000
9:124801413:GGAC:G	acceptor_gain	1.0000
9:124801642:G:GT	donor_gain	1.0000
9:124801659:GGCAG:G	donor_gain	1.0000
9:124801660:GCAGG:G	donor_gain	1.0000
9:124801664:G:GG	donor_gain	1.0000
9:124801665:T:A	donor_loss	1.0000
9:124807776:CACA:C	acceptor_loss	1.0000
9:124807778:CAG:C	acceptor_loss	1.0000
9:124807779:A:AG	acceptor_gain	1.0000
9:124807779:AGG:A	acceptor_loss	1.0000
9:124807780:G:GG	acceptor_gain	1.0000
9:124807780:GGCA:G	acceptor_gain	1.0000
9:124807962:GCAAG:G	donor_gain	1.0000
9:124807963:CAAGG:C	donor_loss	1.0000
9:124807965:AGGT:A	donor_loss	1.0000
9:124807966:GG:G	donor_loss	1.0000
9:124807967:GTC:G	donor_loss	1.0000
9:124807968:T:G	donor_loss	1.0000
9:124777361:G:GG	donor_gain	0.9900

AlphaMissense

4252 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:124807864:T:A	W418R	0.999
9:124807864:T:C	W418R	0.999
9:124807931:T:C	L440P	0.999
9:124807939:T:C	F443L	0.999
9:124807941:C:A	F443L	0.999
9:124807941:C:G	F443L	0.999
9:124809843:T:A	W464R	0.999
9:124809843:T:C	W464R	0.999
9:124810365:T:A	W638R	0.999
9:124810365:T:C	W638R	0.999
9:124787035:T:A	C51S	0.998
9:124787035:T:C	C51R	0.998
9:124787036:G:C	C51S	0.998
9:124787152:T:A	C90S	0.998
9:124787152:T:C	C90R	0.998
9:124787153:G:A	C90Y	0.998
9:124787153:G:C	C90S	0.998
9:124787154:T:G	C90W	0.998
9:124807866:G:C	W418C	0.998
9:124807866:G:T	W418C	0.998
9:124807904:T:A	V431D	0.998
9:124807940:T:C	F443S	0.998
9:124807958:T:C	F449S	0.998
9:124809885:T:G	Y478D	0.998
9:124809918:T:G	Y489D	0.998
9:124810367:G:C	W638C	0.998
9:124810367:G:T	W638C	0.998
9:124787025:C:G	C47W	0.997
9:124787029:T:A	C49S	0.997
9:124787029:T:C	C49R	0.997

dbSNP variants (sampled 300 via entrez): RS1000175242 (9:124810583 T>G), RS1000291329 (9:124810767 C>A), RS1000339169 (9:124797974 AAGG>A), RS1000375878 (9:124780501 G>A), RS1000391465 (9:124798364 T>C), RS1000406748 (9:124805190 C>T), RS1000482395 (9:124799810 G>C), RS1000585022 (9:124811036 C>G), RS1000714944 (9:124787164 C>G), RS1000723261 (9:124799514 G>C), RS1000756558 (9:124805422 C>T), RS1000881552 (9:124780710 C>T), RS1000922884 (9:124805410 A>G), RS1000966097 (9:124793573 T>C), RS1001103368 (9:124786850 C>T)

Disease associations

OMIM: gene MIM:615899 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST007354_8	Intracranial aneurysm	2.000000e-19

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects cotreatment, increases expression, affects expression	7
Particulate Matter	decreases expression, increases abundance, affects cotreatment, increases expression	5
Cadmium Chloride	increases abundance, increases expression, decreases expression	4
Tobacco Smoke Pollution	decreases expression	3
bisphenol A	increases expression, affects cotreatment, decreases expression	2
sodium arsenite	decreases expression, increases expression	2
entinostat	increases expression, affects cotreatment	2
Cadmium	decreases expression, increases abundance	2
Nickel	decreases expression	2
Silicon Dioxide	decreases expression	2
methyleugenol	decreases expression	1
methylselenic acid	increases expression	1
terbufos	increases methylation	1
trichostatin A	increases expression	1
4-chloro-1,2-diaminobenzene	affects response to substance	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cupric oxide	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
MRK 003	decreases expression	1
jinfukang	increases expression	1
NSC 689534	increases expression	1
Temozolomide	decreases expression	1
Arsenic Trioxide	increases expression	1
Vorinostat	increases expression	1
Air Pollutants	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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