VMO1

Summary

VMO1 (vitelline membrane outer layer 1 homolog, HGNC:30387) is a protein-coding gene on chromosome 17p13.2, encoding Vitelline membrane outer layer protein 1 homolog (Q7Z5L0).

Located in extracellular exosome.

Source: NCBI Gene 284013 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_182566

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30387
Approved symbol	VMO1
Name	vitelline membrane outer layer 1 homolog
Location	17p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000182853
Ensembl biotype	protein_coding
OMIM	621110
Entrez	284013

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000328739, ENST00000354194, ENST00000416307, ENST00000441199

RefSeq mRNA: 4 — MANE Select: NM_182566 NM_001144939, NM_001144940, NM_001144941, NM_182566

CCDS: CCDS11055, CCDS45585, CCDS45586, CCDS45587

Canonical transcript exons

ENST00000328739 — 3 exons

Exon	Start	End
ENSE00001331103	4785937	4786052
ENSE00002640103	4786158	4786364
ENSE00003464273	4785285	4785659

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 99.23.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6852 / max 107.8678, expressed in 210 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
163963	0.6371	197
163964	0.0481	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
nasal cavity epithelium	UBERON:0005384	99.23	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	99.04	gold quality
nasal cavity mucosa	UBERON:0001826	97.19	gold quality
palpebral conjunctiva	UBERON:0001812	95.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	95.64	gold quality
mucosa of paranasal sinus	UBERON:0005030	91.25	gold quality
bronchial epithelial cell	CL:0002328	86.63	gold quality
pituitary gland	UBERON:0000007	85.92	gold quality
bronchus	UBERON:0002185	85.75	gold quality
adenohypophysis	UBERON:0002196	84.78	gold quality
spleen	UBERON:0002106	84.13	gold quality
right lobe of liver	UBERON:0001114	83.08	gold quality
descending thoracic aorta	UBERON:0002345	79.83	gold quality
right coronary artery	UBERON:0001625	79.62	gold quality
thoracic aorta	UBERON:0001515	76.90	gold quality
ascending aorta	UBERON:0001496	76.87	gold quality
granulocyte	CL:0000094	75.86	gold quality
vermiform appendix	UBERON:0001154	75.10	gold quality
liver	UBERON:0002107	75.09	gold quality
right lung	UBERON:0002167	75.06	gold quality
left coronary artery	UBERON:0001626	74.99	gold quality
upper lobe of left lung	UBERON:0008952	74.53	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	74.37	gold quality
coronary artery	UBERON:0001621	74.30	gold quality
upper arm skin	UBERON:0004263	74.26	gold quality
omental fat pad	UBERON:0010414	72.97	gold quality
peritoneum	UBERON:0002358	72.92	gold quality
spinal cord	UBERON:0002240	72.73	gold quality
aorta	UBERON:0000947	72.57	gold quality
endothelial cell	CL:0000115	72.52	silver quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-13	yes	3911.58
E-CURD-79	yes	673.69
E-MTAB-8142	yes	90.81
E-CURD-114	yes	54.07
E-CURD-53	no	101.54
E-MTAB-8060	no	32.82
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Methylation and transcriptome analyses construct a prognostic model and reveal the suppressor role of VMO1 in lung adenocarcinoma. (PMID:39053673)

Cross-species orthologs

18 orthologs

Organism	Symbol	Gene ID
danio_rerio	vmo1a	ENSDARG00000043002
danio_rerio	vmo1b	ENSDARG00000045299
mus_musculus	Vmo1	ENSMUSG00000020830
rattus_norvegicus	Vmo1	ENSRNOG00000026508
caenorhabditis_elegans		WBGENE00007674
caenorhabditis_elegans		WBGENE00008129
caenorhabditis_elegans		WBGENE00012631
caenorhabditis_elegans		WBGENE00013194
caenorhabditis_elegans		WBGENE00013290
caenorhabditis_elegans		WBGENE00017876
caenorhabditis_elegans		WBGENE00018504
caenorhabditis_elegans		WBGENE00020174
caenorhabditis_elegans		WBGENE00020177
caenorhabditis_elegans		WBGENE00020179
caenorhabditis_elegans		WBGENE00021176
caenorhabditis_elegans		WBGENE00021434
caenorhabditis_elegans		WBGENE00021457
caenorhabditis_elegans		WBGENE00021494

Protein

Protein identifiers

Vitelline membrane outer layer protein 1 homolog — Q7Z5L0 (reviewed: Q7Z5L0)

All UniProt accessions (1): Q7Z5L0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the VMO1 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q7Z5L0-1	1	yes
Q7Z5L0-2	2
Q7Z5L0-3	3
Q7Z5L0-4	4

RefSeq proteins (4): NP_001138411, NP_001138412, NP_001138413, NP_872372* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005515	VOMI	Family
IPR036706	VOMI_sf	Homologous_superfamily

Pfam: PF03762

UniProt features (12 total): disulfide bond 4, splice variant 4, sequence variant 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z5L0-F1	82.91	0.56

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 (4): 53–86, 114–146, 169–199, 174–200

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE11864_CSF1_VS_CSF1_IFNG_IN_MAC_UP, GSE11864_CSF1_IFNG_VS_CSF1_PAM3CYS_IN_MAC_DN, BLANCO_MELO_HUMAN_PARAINFLUENZA_VIRUS_3_INFECTION_A594_CELLS_DN, BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_DN, HAY_BONE_MARROW_MONOCYTE, DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_SUSTENTACULAR_CELLS, DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_BOWMANS_GLAND, DESCARTES_MAIN_FETAL_SLC26A4_PAEP_POSITIVE_CELLS, DESCARTES_FETAL_ADRENAL_SLC26A4_PAEP_POSITIVE_CELLS, DESCARTES_FETAL_INTESTINE_MYELOID_CELLS, DESCARTES_FETAL_MUSCLE_SKELETAL_MUSCLE_CELLS, SOBOLEV_PBMC_PANDEMRIX_AGE_18_64YO_MEDIUM_HIGH_ADVERSE_EVENT_SUBJECTS_1DY_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): obsolete extracellular space (GO:0005615), extracellular exosome (GO:0070062), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
extracellular vesicle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

868 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VMO1	TMEM200A	Q86VY9	466
VMO1	EFHC1	Q5JVL4	454
VMO1	TMEM252	Q8N6L7	421
VMO1	SPEF1	Q9Y4P9	406
VMO1	STYXL1	Q9Y6J8	390
VMO1	GUCY1A2	P33402	376
VMO1	GRAMD2A	Q8IUY3	376
VMO1	NEK11	Q8NG66	374
VMO1	TTLL9	Q3SXZ7	372
VMO1	CHID1	Q9BWS9	368
VMO1	PI4KA	P42356	358
VMO1	LINGO2	Q7L985	355
VMO1	RPL4	P36578	354
VMO1	MATN4	O95460	354
VMO1	BORCS6	Q96GS4	350

IntAct

2 interactions, top by confidence:

A	B	Type	Score
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A2WMH2, A2WPN7, C0HK14, D9UBG0, D9UBI3, F4HQX1, F4I837, F4I9R6, F4IB94, F4IB95, H3JUC3, O04313, O04314, O60844, O80736, O80737, O80948, O80950, O80998, P0C5C6, P15501, P18670, P18674, P41366, P82859, P82953, P84801, P93114, Q0JMY8, Q5SXG7, Q5U9T2, Q5XF82, Q7Z5L0, Q8CJD3, Q8GWI7, Q8K0C5, Q96DA0, Q9FFW6, Q9FFW7, Q9FGC4

Diamond homologs: P41366, Q5SXG7, Q7Z5L0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

491 predictions. Top by Δscore:

Variant	Effect	Δscore
17:4786142:ACG:A	donor_gain	1.0000
17:4786143:CGC:C	donor_gain	1.0000
17:4786243:T:TA	donor_gain	1.0000
17:4785900:CCA:C	donor_gain	0.9900
17:4785939:T:TA	donor_gain	0.9900
17:4785956:C:CT	donor_gain	0.9900
17:4785966:ATTG:A	donor_gain	0.9900
17:4785969:G:A	donor_gain	0.9900
17:4785980:T:A	donor_gain	0.9900
17:4785655:CCCAG:C	acceptor_gain	0.9800
17:4785656:CCAGC:C	acceptor_gain	0.9800
17:4785657:CAG:C	acceptor_gain	0.9800
17:4785952:TCTAC:T	donor_gain	0.9800
17:4785953:CTACC:C	donor_gain	0.9800
17:4786143:CG:C	donor_gain	0.9800
17:4786240:A:AC	donor_gain	0.9800
17:4786241:C:CC	donor_gain	0.9800
17:4785656:CCAG:C	acceptor_gain	0.9700
17:4785657:CAGC:C	acceptor_gain	0.9700
17:4785957:C:CT	donor_gain	0.9700
17:4786142:A:AC	donor_gain	0.9700
17:4786143:C:CC	donor_gain	0.9700
17:4785956:CCA:C	donor_gain	0.9600
17:4785660:C:CC	acceptor_gain	0.9500
17:4785962:G:A	donor_gain	0.9500
17:4786199:T:C	donor_gain	0.9500
17:4786237:G:C	donor_gain	0.9500
17:4786242:T:C	donor_gain	0.9500
17:4786234:CTGG:C	donor_gain	0.9400
17:4786235:TGGT:T	donor_gain	0.9400

AlphaMissense

1300 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:4785647:C:A	W108C	0.992
17:4785647:C:G	W108C	0.992
17:4786212:C:A	W47C	0.984
17:4786212:C:G	W47C	0.984
17:4786167:G:C	F62L	0.978
17:4786167:G:T	F62L	0.978
17:4786169:A:G	F62L	0.978
17:4785655:C:A	G106C	0.973
17:4785649:A:G	W108R	0.972
17:4785649:A:T	W108R	0.972
17:4786158:C:A	K65N	0.972
17:4786158:C:G	K65N	0.972
17:4786003:A:G	I82T	0.970
17:4785485:A:C	F162L	0.968
17:4785485:A:T	F162L	0.968
17:4785487:A:G	F162L	0.968
17:4785602:G:C	F123L	0.967
17:4785602:G:T	F123L	0.967
17:4785604:A:G	F123L	0.967
17:4785601:A:G	S124P	0.966
17:4785607:C:G	A122P	0.965
17:4785548:G:C	N141K	0.962
17:4785548:G:T	N141K	0.962
17:4785476:C:A	W165C	0.961
17:4785476:C:G	W165C	0.961
17:4786168:A:G	F62S	0.960
17:4785473:A:C	S166R	0.959
17:4785473:A:T	S166R	0.959
17:4785475:T:G	S166R	0.959
17:4785540:A:G	F144S	0.958

dbSNP variants (sampled 300 via entrez): RS1000237291 (17:4786975 C>A,G,T), RS1000458431 (17:4786668 G>T), RS1000466331 (17:4788081 C>T), RS1002404578 (17:4786645 A>T), RS1003254595 (17:4784907 G>A), RS1004259766 (17:4786197 C>A,T), RS1005237270 (17:4787308 C>T), RS1006252665 (17:4787073 C>G), RS1008565068 (17:4785822 G>A,C,T), RS1009095556 (17:4786703 G>T), RS1010192137 (17:4786595 T>C), RS1010789625 (17:4785207 C>G,T), RS1011968360 (17:4785168 A>G), RS1013391596 (17:4786539 G>A), RS1013980289 (17:4787971 C>T)

Disease associations

OMIM: gene MIM:621110 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	affects expression, decreases expression	2
versicolorin A	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
2,2’,4,4’,5-brominated diphenyl ether	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
licochalcone B	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	decreases expression	1
Glyphosate	affects methylation	1
Benzene	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Camptothecin	increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Estradiol	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Valproic Acid	increases methylation	1
8-Bromo Cyclic Adenosine Monophosphate	increases expression	1
Medroxyprogesterone Acetate	decreases expression	1

Clinical trials (associated diseases)

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