VXN

Summary

VXN (vexin, HGNC:28498) is a protein-coding gene on chromosome 8q13.1, encoding Vexin (Q8TAG6). Required for neurogenesis in the neural plate and retina.

Predicted to be involved in neuron differentiation. Predicted to be located in nucleus and plasma membrane.

Source: NCBI Gene 254778 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_152765

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28498
Approved symbol	VXN
Name	vexin
Location	8q13.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC33510
Ensembl gene	ENSG00000169085
Ensembl biotype	protein_coding
Entrez	254778

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000305454, ENST00000450307, ENST00000460144, ENST00000480005, ENST00000484919, ENST00000485639, ENST00000488582, ENST00000521495, ENST00000521813, ENST00000522977, ENST00000699189

RefSeq mRNA: 1 — MANE Select: NM_152765 NM_152765

CCDS: CCDS6191

Canonical transcript exons

ENST00000305454 — 6 exons

Exon	Start	End
ENSE00003529292	66510096	66510157
ENSE00003560783	66513540	66513637
ENSE00003584377	66496437	66496492
ENSE00003639395	66515893	66518524
ENSE00003642610	66505375	66505528
ENSE00003975900	66493566	66493718

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 96.83.

FANTOM5 (CAGE): breadth broad, TPM avg 5.2254 / max 1909.0307, expressed in 201 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
89197	1.5500	98
89203	1.5422	128
89202	0.7870	93
89206	0.5313	100
89198	0.2024	47
89199	0.1411	54
89201	0.1149	56
89200	0.1109	55
89205	0.0839	50
205215	0.0612	31

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	96.83	gold quality
prefrontal cortex	UBERON:0000451	96.80	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.80	gold quality
anterior cingulate cortex	UBERON:0009835	96.30	gold quality
right frontal lobe	UBERON:0002810	95.52	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	94.28	gold quality
amygdala	UBERON:0001876	92.32	gold quality
spinal cord	UBERON:0002240	91.69	gold quality
frontal cortex	UBERON:0001870	91.43	gold quality
frontal lobe	UBERON:0016525	91.43	gold quality
caudate nucleus	UBERON:0001873	91.12	gold quality
neocortex	UBERON:0001950	90.60	gold quality
putamen	UBERON:0001874	89.68	gold quality
hypothalamus	UBERON:0001898	89.07	gold quality
nucleus accumbens	UBERON:0001882	88.85	gold quality
cerebral cortex	UBERON:0000956	88.22	gold quality
telencephalon	UBERON:0001893	87.65	gold quality
Ammon’s horn	UBERON:0001954	87.11	gold quality
calcaneal tendon	UBERON:0003701	87.11	gold quality
forebrain	UBERON:0001890	83.74	gold quality
substantia nigra	UBERON:0002038	83.38	gold quality
brain	UBERON:0000955	81.67	gold quality
temporal lobe	UBERON:0001871	80.78	gold quality
Brodmann (1909) area 46	UBERON:0006483	79.77	gold quality
mucosa of stomach	UBERON:0001199	78.87	gold quality
midbrain	UBERON:0001891	78.45	gold quality
corpus callosum	UBERON:0002336	77.63	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.96	gold quality
postcentral gyrus	UBERON:0002581	75.60	gold quality
superior frontal gyrus	UBERON:0002661	75.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-98556	yes	721.27
E-GEOD-100618	yes	167.85
E-ANND-3	yes	3.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

126 targeting VXN, 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-3646	100.00	73.56	5283
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-7978	99.86	66.90	856
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-3681-5P	99.82	66.88	387
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-4659A-3P	99.80	72.62	4248

Literature-anchored findings (GeneRIF, showing 1)

• Vexin is upregulated in cerebral cortical neurons by brain-derived neurotrophic factor. (PMID:32558188)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Vxn	ENSMUSG00000067879
rattus_norvegicus	Vxn	ENSRNOG00000021663

Protein

Protein identifiers

Vexin — Q8TAG6 (reviewed: Q8TAG6)

All UniProt accessions (5): Q8TAG6, E5RH60, E5RJS6, E5RKA6, R4GNJ7

UniProt curated annotations — full annotation on UniProt →

Function. Required for neurogenesis in the neural plate and retina. Strongly cooperates with neural bHLH factors to promote neurogenesis.

Subcellular location. Cell membrane. Nucleus.

Similarity. Belongs to the vexin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8TAG6-1	1	yes
Q8TAG6-2	2

RefSeq proteins (1): NP_689978* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027900	Vexin_dom	Domain
IPR040470	Vexin	Family

Pfam: PF15505

UniProt features (4 total): chain 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAG6-F1	60.95	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): GOBP_NEUROGENESIS, MEF2_02, CAGCTG_AP4_Q5, TCF4_Q5, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, ISRE_01, chr8q13, HARRIS_BRAIN_CANCER_PROGENITORS, CTGAGCC_MIR24, MEF2_03, ZHENG_GLIOBLASTOMA_PLASTICITY_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, RATTENBACHER_BOUND_BY_CELF1, CENPT_TARGET_GENES

GO Biological Process (3): neurogenesis (GO:0022008), neuron differentiation (GO:0030182), nervous system development (GO:0007399)

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

GO Cellular Component (3): nucleus (GO:0005634), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell differentiation	2
nervous system development	1
generation of neurons	1
system development	1
binding	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

446 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VXN	FAM227B	Q96M60	615
VXN	RNF144A	P50876	443
VXN	C8orf48	Q96LL4	435
VXN	OR2T2	Q6IF00	371
VXN	RAD9B	Q6WBX8	370
VXN	KIFC3	Q9BVG8	369
VXN	TMEM126B	Q8IUX1	362
VXN	MYBL1	P10243	351
VXN	ZCCHC18	P0CG32	350
VXN	SPACA9	Q96E40	349
VXN	RAVER2	Q9HCJ3	348
VXN	XPO4	Q9C0E2	345
VXN	NOL4L	Q96MY1	323
VXN	GET4	Q7L5D6	317
VXN	GTF3C6	Q969F1	311

IntAct

17 interactions, top by confidence:

A	B	Type	Score
CEP70	VXN	psi-mi:“MI:0915”(physical association)	0.560
ZNF76	VXN	psi-mi:“MI:0915”(physical association)	0.560
VXN	CABP2	psi-mi:“MI:0915”(physical association)	0.560
VXN	NTAQ1	psi-mi:“MI:0915”(physical association)	0.560
FHL2	VXN	psi-mi:“MI:0915”(physical association)	0.560
TRIM61	VXN	psi-mi:“MI:0915”(physical association)	0.400
VXN	CEP70	psi-mi:“MI:0915”(physical association)	0.000
NTAQ1	VXN	psi-mi:“MI:0915”(physical association)	0.000
FHL2	VXN	psi-mi:“MI:0915”(physical association)	0.000
ZNF76	VXN	psi-mi:“MI:0915”(physical association)	0.000
CABP2	VXN	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): C8orf46 (Two-hybrid), C8orf46 (Two-hybrid), C8orf46 (Two-hybrid), C8orf46 (Two-hybrid), C8orf46 (Two-hybrid), C8orf46 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQF7, A6YQT5, O54842, O60356, O82286, P03131, P03238, P04602, P04605, P05909, P06937, P09267, P0C765, P17759, P18098, P19847, P23057, P24103, P24820, P27224, P27261, P27445, P35959, P50445, P54092, P54093, P69484, P69485, Q00039, Q06658, Q0VCV7, Q1X709, Q1X711, Q32LJ5, Q4JQX3, Q5R5R7, Q67684, Q8B912, Q8BG31, Q8C3M9

Diamond homologs: Q0VCV7, Q5R5R7, Q8BG31, Q8TAG6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1016 predictions. Top by Δscore:

Variant	Effect	Δscore
8:66496432:TGCA:T	acceptor_loss	1.0000
8:66496433:GCA:G	acceptor_loss	1.0000
8:66496435:A:AG	acceptor_gain	1.0000
8:66496435:A:T	acceptor_loss	1.0000
8:66496436:G:A	acceptor_loss	1.0000
8:66496436:G:GT	acceptor_gain	1.0000
8:66496436:GT:G	acceptor_gain	1.0000
8:66496436:GTA:G	acceptor_gain	1.0000
8:66496436:GTAT:G	acceptor_gain	1.0000
8:66496436:GTATC:G	acceptor_gain	1.0000
8:66496488:AGAAT:A	donor_gain	1.0000
8:66496489:GAAT:G	donor_gain	1.0000
8:66496489:GAATG:G	donor_gain	1.0000
8:66496491:AT:A	donor_gain	1.0000
8:66496493:G:GG	donor_gain	1.0000
8:66505526:CCGG:C	donor_loss	1.0000
8:66505529:GT:G	donor_loss	1.0000
8:66505530:T:A	donor_loss	1.0000
8:66510094:A:AG	acceptor_gain	1.0000
8:66510095:G:GG	acceptor_gain	1.0000
8:66513535:GACA:G	acceptor_loss	1.0000
8:66513536:ACAG:A	acceptor_loss	1.0000
8:66513537:CA:C	acceptor_loss	1.0000
8:66513538:A:AG	acceptor_gain	1.0000
8:66513539:G:A	acceptor_loss	1.0000
8:66513539:G:GG	acceptor_gain	1.0000
8:66513634:GAGG:G	donor_gain	1.0000
8:66513636:GG:G	donor_gain	1.0000
8:66513637:GG:G	donor_gain	1.0000
8:66493717:GG:G	donor_gain	0.9900

AlphaMissense

1321 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:66493694:T:C	F16L	0.999
8:66493696:C:A	F16L	0.999
8:66493696:C:G	F16L	0.999
8:66516062:T:C	F204L	0.998
8:66516064:T:A	F204L	0.998
8:66516064:T:G	F204L	0.998
8:66493662:T:C	I5T	0.996
8:66493695:T:C	F16S	0.994
8:66516063:T:C	F204S	0.994
8:66493662:T:G	I5S	0.993
8:66516055:C:A	N201K	0.992
8:66516055:C:G	N201K	0.992
8:66516063:T:G	F204C	0.992
8:66493664:T:G	Y6D	0.991
8:66493695:T:G	F16C	0.990
8:66493662:T:A	I5N	0.989
8:66493680:A:T	E11V	0.988
8:66516062:T:A	F204I	0.988
8:66493664:T:C	Y6H	0.987
8:66493698:C:T	T17I	0.987
8:66516051:C:T	T200I	0.987
8:66493686:T:A	I13K	0.986
8:66493694:T:A	F16I	0.985
8:66493694:T:G	F16V	0.985
8:66493664:T:A	Y6N	0.984
8:66493686:T:G	I13R	0.984
8:66516000:T:A	L183H	0.984
8:66516045:G:A	G198E	0.984
8:66493707:T:C	I20T	0.983
8:66516044:G:A	G198R	0.983

dbSNP variants (sampled 300 via entrez): RS1000066410 (8:66504233 G>A,C), RS1000348101 (8:66499244 G>C,T), RS1000686423 (8:66514537 A>G), RS1000709993 (8:66517541 T>A,C), RS1000951177 (8:66506225 G>C), RS1000991388 (8:66517856 C>T), RS1001073959 (8:66491939 A>T), RS1001230063 (8:66505446 C>A,T), RS1001306261 (8:66492456 A>G), RS1001369773 (8:66497855 C>A), RS1001372099 (8:66516785 C>T), RS1001410994 (8:66499138 T>C), RS1001541144 (8:66500170 A>G), RS1001587164 (8:66492688 T>C), RS1001791268 (8:66494320 G>A,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

2 associations (top):

Study	Trait	p-value
GCST008103_169	Bipolar disorder	7.000000e-06
GCST008115_21	Bipolar I disorder	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009963	bipolar I disorder

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
Estradiol	affects binding, increases expression, affects cotreatment	3
Valproic Acid	decreases expression	2
perfluorooctane sulfonic acid	decreases expression	1
entinostat	decreases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Coumestrol	affects cotreatment, increases expression	1
Lead	affects expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Vanadates	decreases expression	1
Aflatoxin B1	decreases expression	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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