PLXNB3

Summary

PLXNB3 (plexin B3, HGNC:9105) is a protein-coding gene on chromosome Xq28, encoding Plexin-B3 (Q9ULL4). Receptor for SEMA5A that plays a role in axon guidance, invasive growth and cell migration.

The protein encoded by this gene is a member of the plexin family. It functions as a receptor for semaphorin 5A, and plays a role in axon guidance, invasive growth and cell migration. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 5365 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 490 total — 2 pathogenic
• MANE Select transcript: NM_005393

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9105
Approved symbol	PLXNB3
Name	plexin B3
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	PLEXR, PLEXB3
Ensembl gene	ENSG00000198753
Ensembl biotype	protein_coding
OMIM	300214
Entrez	5365

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000361971, ENST00000411613, ENST00000448847, ENST00000455214, ENST00000469190, ENST00000472415, ENST00000482654, ENST00000485980, ENST00000538966, ENST00000902319, ENST00000902320, ENST00000930103, ENST00000943382, ENST00000943383, ENST00000943384

RefSeq mRNA: 2 — MANE Select: NM_005393 NM_001163257, NM_005393

CCDS: CCDS14729, CCDS55536

Canonical transcript exons

ENST00000361971 — 36 exons

Exon	Start	End
ENSE00000677948	153768249	153768428
ENSE00000677949	153768948	153769076
ENSE00000868275	153766873	153767913
ENSE00000868276	153769162	153769262
ENSE00000868277	153769807	153769939
ENSE00000868278	153770092	153770248
ENSE00000868279	153770338	153770446
ENSE00000868280	153770528	153770642
ENSE00000868281	153770758	153770883
ENSE00000868283	153771310	153771403
ENSE00000868284	153771486	153771655
ENSE00000868285	153771864	153772015
ENSE00000868286	153772182	153772287
ENSE00000868287	153772886	153773016
ENSE00000868288	153773230	153773406
ENSE00000868289	153773518	153773713
ENSE00000868290	153773859	153774098
ENSE00000868291	153774186	153774344
ENSE00000868292	153774420	153774571
ENSE00000868293	153774706	153774806
ENSE00000868294	153774880	153775103
ENSE00000868295	153775225	153775403
ENSE00000868298	153776356	153776459
ENSE00000868302	153777948	153778095
ENSE00000868303	153778261	153778325
ENSE00001372409	153764249	153764304
ENSE00001919533	153778935	153779341
ENSE00003493941	153777528	153777688
ENSE00003495747	153778600	153778674
ENSE00003523666	153778396	153778471
ENSE00003525255	153775887	153776214
ENSE00003542593	153777208	153777380
ENSE00003593190	153775594	153775660
ENSE00003608758	153770965	153771081
ENSE00003655422	153765471	153765580
ENSE00003681018	153776887	153776980

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 98.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.7933 / max 381.3294, expressed in 1147 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
198099	5.4423	1106
198100	2.3510	295

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	98.43	gold quality
tibial nerve	UBERON:0001323	97.95	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.41	gold quality
Ammon’s horn	UBERON:0001954	97.33	gold quality
substantia nigra	UBERON:0002038	97.21	gold quality
putamen	UBERON:0001874	96.96	gold quality
primary visual cortex	UBERON:0002436	96.96	gold quality
temporal lobe	UBERON:0001871	96.89	gold quality
amygdala	UBERON:0001876	96.89	gold quality
cerebellar hemisphere	UBERON:0002245	96.81	gold quality
cerebellar cortex	UBERON:0002129	96.78	gold quality
cerebellum	UBERON:0002037	96.77	gold quality
caudate nucleus	UBERON:0001873	95.97	gold quality
right frontal lobe	UBERON:0002810	95.56	gold quality
sural nerve	UBERON:0015488	95.50	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.31	gold quality
corpus callosum	UBERON:0002336	95.22	gold quality
nucleus accumbens	UBERON:0001882	95.12	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.50	gold quality
hypothalamus	UBERON:0001898	94.23	gold quality
left adrenal gland cortex	UBERON:0035825	93.91	gold quality
right adrenal gland cortex	UBERON:0035827	93.70	gold quality
right adrenal gland	UBERON:0001233	93.55	gold quality
left adrenal gland	UBERON:0001234	93.35	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.22	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.05	gold quality
anterior cingulate cortex	UBERON:0009835	92.97	gold quality
brain	UBERON:0000955	92.74	gold quality
cerebral cortex	UBERON:0000956	92.63	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.59	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.19

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF, ESR2

miRNA regulators (miRDB)

27 targeting PLXNB3, 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-3163	100.00	77.23	8605
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-8070	99.07	69.30	1303
HSA-MIR-4742-5P	98.89	68.41	1542
HSA-MIR-6887-5P	98.56	68.49	1295
HSA-MIR-6795-5P	98.52	68.51	1277
HSA-MIR-338-3P	98.14	67.38	1137
HSA-MIR-4736	97.96	65.89	1287
HSA-MIR-3165	96.18	66.22	473

Literature-anchored findings (GeneRIF, showing 10)

• Plexin-B3 is a functional receptor for semaphorin 5A (PMID:15218527)
• Data suggest an involvement of homophilic interaction of B3 in semaphorin-independent signaling mechanisms positively influencing neuronal morphogenesis or function. (PMID:16122393)
• plexin B3 may influence cognitive performance, and the development of white matter in vivo in a way similar to its known stimulating effect on neurite outgrowth in vitro (PMID:17033634)
• A virtual expression database search and RT-PCR analysis showed co-expression of SEMA5A and Plexin B3, and the interaction of SEMA5A with Plexin B3 was confirmed by co-immunoprecipitation studies. (PMID:19329067)
• Data represent a novel signaling of semaphorin 5A and plexin B3 in the control of cell motility by indirect inactivation of Rac1 through RhoGDIalpha. (PMID:20696765)
• Data show that Semaphorin 5A (Sema5A) and plexin-B3 inhibit glioma cell invasion through Rac1 inactivation. (PMID:21706053)
• Essential roles of plexin-B3(+) oligodendrocyte precursor cells in the pathogenesis of Alzheimer’s disease. (PMID:34267322)
• Glycoproteomics Identifies Plexin-B3 as a Targetable Cell Surface Protein Required for the Growth and Invasion of Triple-Negative Breast Cancer Cells. (PMID:35981243)
• SEMA5A-PLXNB3 Axis Promotes PDAC Liver Metastasis Outgrowth through Enhancing the Warburg Effect. (PMID:36741230)
• Plexin-B3 expression stimulates MET signaling, breast cancer stem cell specification, and lung metastasis. (PMID:36857181)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	plxnb3	ENSDARG00000032990
mus_musculus	Plxnb3	ENSMUSG00000031385
rattus_norvegicus	Plxnb3	ENSRNOG00000061731
drosophila_melanogaster	PlexB	FBGN0025740
drosophila_melanogaster	PlexA	FBGN0025741
caenorhabditis_elegans		WBGENE00004047
caenorhabditis_elegans		WBGENE00004048

Paralogs (8): PLXND1 (ENSG00000004399), PLXNA2 (ENSG00000076356), PLXNA1 (ENSG00000114554), PLXNA3 (ENSG00000130827), PLXNC1 (ENSG00000136040), PLXNB1 (ENSG00000164050), PLXNB2 (ENSG00000196576), PLXNA4 (ENSG00000221866)

Protein

Protein identifiers

Plexin-B3 — Q9ULL4 (reviewed: Q9ULL4)

All UniProt accessions (4): Q9ULL4, H7BZV5, H7C0P4, H7C3L0

UniProt curated annotations — full annotation on UniProt →

Function. Receptor for SEMA5A that plays a role in axon guidance, invasive growth and cell migration. Stimulates neurite outgrowth and mediates Ca(2+)/Mg(2+)-dependent cell aggregation. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1.

Subunit / interactions. Interacts (via cytoplasmic domain) with RAC1 and ARHGDIA. Binds MET and MST1R. Interacts (via cytoplasmic domain) with FSCN1. Interacts with RIT2/RIN. May form homodimers (via Sema domain).

Subcellular location. Cell membrane.

Tissue specificity. Expression detected in Purkinje and granular cells in cerebellum, and in brain neocortex but not in corpus callosum. Expressed in glioma cells and embryonic kidney cells (at protein level). Expressed in brain, liver, pancreas and placenta, with weak expression detected also in lung and kidney. Expressed in several glioma cell lines.

Similarity. Belongs to the plexin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9ULL4-1	1	yes
Q9ULL4-2	2

RefSeq proteins (2): NP_001156729, NP_005384* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001627	Semap_dom	Domain
IPR002165	Plexin_repeat	Repeat
IPR002909	IPT_dom	Domain
IPR008936	Rho_GTPase_activation_prot	Homologous_superfamily
IPR013548	Plexin_cytoplasmic_RasGAP_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR014756	Ig_E-set	Homologous_superfamily
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR016201	PSI	Domain
IPR031148	Plexin	Family
IPR036352	Semap_dom_sf	Homologous_superfamily
IPR041019	TIG1_plexin	Domain
IPR041362	TIG2_plexin	Domain
IPR046800	Plexin_RBD	Domain
IPR057533	PSI_Plexin-B	Domain

Pfam: PF01403, PF01437, PF01833, PF08337, PF17960, PF18020, PF20170, PF24317, PF24479

UniProt features (40 total): disulfide bond 10, domain 8, glycosylation site 8, sequence variant 6, topological domain 2, sequence conflict 2, signal peptide 1, chain 1, transmembrane region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULL4-F1	81.47	0.32

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 (10): 98–107, 132–140, 267–370, 283–315, 333–357, 474–491, 480–525, 483–500, 494–506, 562–580

Glycosylation sites (8): 51, 231, 615, 802, 900, 957, 1101, 1218

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-416700	Other semaphorin interactions

MSigDB gene sets: 166 (showing top): GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_CELL_CHEMOTAXIS, GOBP_SYNAPSE_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_HYDROLASE_ACTIVITY, REACTOME_OTHER_SEMAPHORIN_INTERACTIONS, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOCC_CELL_SURFACE, AP4_Q6, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGGTGGRR_PAX4_03, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_LAMELLIPODIUM_ASSEMBLY, CAGCTG_AP4_Q5

GO Biological Process (14): positive regulation of endothelial cell proliferation (GO:0001938), homophilic cell-cell adhesion (GO:0007156), negative regulation of cell adhesion (GO:0007162), synapse assembly (GO:0007416), regulation of cell shape (GO:0008360), negative regulation of lamellipodium assembly (GO:0010593), positive regulation of neuron projection development (GO:0010976), negative regulation of cell migration (GO:0030336), negative regulation of GTPase activity (GO:0034260), positive regulation of axonogenesis (GO:0050772), positive chemotaxis (GO:0050918), cell chemotaxis (GO:0060326), semaphorin-plexin signaling pathway (GO:0071526), nervous system development (GO:0007399)

GO Molecular Function (5): semaphorin receptor activity (GO:0017154), protein domain specific binding (GO:0019904), Rho GDP-dissociation inhibitor binding (GO:0051022), cell-cell adhesion mediator activity (GO:0098632), protein binding (GO:0005515)

GO Cellular Component (4): semaphorin receptor complex (GO:0002116), plasma membrane (GO:0005886), cell surface (GO:0009986), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Semaphorin interactions	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell-cell adhesion	2
positive regulation of cell projection organization	2
cell migration	2
chemotaxis	2
cellular anatomical structure	2
endothelial cell proliferation	1
regulation of endothelial cell proliferation	1
positive regulation of epithelial cell proliferation	1
cell adhesion	1
regulation of cell adhesion	1
negative regulation of cellular process	1
nervous system development	1
cell junction assembly	1
synapse organization	1
regulation of cell morphogenesis	1
regulation of biological quality	1
regulation of lamellipodium assembly	1
lamellipodium assembly	1
negative regulation of plasma membrane bounded cell projection assembly	1
negative regulation of lamellipodium organization	1
regulation of neuron projection development	1
neuron projection development	1
regulation of cell migration	1
negative regulation of cell motility	1
GTPase activity	1
regulation of GTPase activity	1
negative regulation of biological process	1
negative regulation of hydrolase activity	1
axonogenesis	1
positive regulation of neurogenesis	1
regulation of axonogenesis	1
cellular response to chemical stimulus	1
cell surface receptor signaling pathway	1
system development	1
transmembrane signaling receptor activity	1
semaphorin-plexin signaling pathway	1
protein binding	1
GDP-dissociation inhibitor binding	1
cell adhesion mediator activity	1
binding	1

Protein interactions and networks

STRING

1086 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PLXNB3	SEMA5A	Q13591	989
PLXNB3	SEMA4D	Q92854	846
PLXNB3	ARHGEF12	Q9NZN5	779
PLXNB3	SEMA3B	Q13214	728
PLXNB3	BCAP31	P51572	724
PLXNB3	ABCD1	P33897	676
PLXNB3	ABCD2	Q9UBJ2	670
PLXNB3	ACSBG1	Q96GR2	667
PLXNB3	COASY	Q13057	650
PLXNB3	L1CAM	P32004	644
PLXNB3	SEMA5B	Q9P283	642
PLXNB3	HGF	P14210	639
PLXNB3	ABCD3	P28288	639
PLXNB3	ARHGEF11	O15085	609
PLXNB3	SEMA3C	Q99985	581

IntAct

19 interactions, top by confidence:

A	B	Type	Score
PLXNB3	SEMA4D	psi-mi:“MI:0407”(direct interaction)	0.560
MET	PLXNB3	psi-mi:“MI:0915”(physical association)	0.520
MST1R	PLXNB3	psi-mi:“MI:0915”(physical association)	0.520
PLXNB3	SEMA4A	psi-mi:“MI:0407”(direct interaction)	0.440
FSCN1	PLXNB3	psi-mi:“MI:0915”(physical association)	0.400
PLXNB3	FSCN1	psi-mi:“MI:0915”(physical association)	0.400
PLXNB3	CUL7	psi-mi:“MI:0915”(physical association)	0.370
PLXNB3	SPOCK2	psi-mi:“MI:0915”(physical association)	0.370
PLXNB3	ARHGEF11	psi-mi:“MI:0915”(physical association)	0.370
PLXNB3	MAGI2	psi-mi:“MI:0915”(physical association)	0.370
PLXNB3	CUL9	psi-mi:“MI:0915”(physical association)	0.370
PLXNB3	BTBD3	psi-mi:“MI:0915”(physical association)	0.370
PLXNB3	MAGI3	psi-mi:“MI:0915”(physical association)	0.370
DSCR9	PLXNB3	psi-mi:“MI:0915”(physical association)	0.000
HSPA13	PLXNB3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): PLXNB3 (Two-hybrid), PLXNB3 (Affinity Capture-MS), PLXNB3 (Affinity Capture-Western), PLXNB3 (Two-hybrid), PLXNB3 (Two-hybrid), TMF1 (Cross-Linking-MS (XL-MS)), CUL7 (Two-hybrid), SPOCK2 (Two-hybrid), ARHGEF11 (Two-hybrid), MAGI2 (Two-hybrid), BTBD3 (Two-hybrid), MAGI3 (Two-hybrid)

ESM2 similar proteins: A0JND9, D3YTS9, O19058, O35795, O55026, O75173, P08648, P11117, P17405, P20611, P21217, P24638, P29376, P56433, Q04519, Q0P5F0, Q0V8G3, Q0VD19, Q11128, Q11131, Q32M88, Q4R5N9, Q4R942, Q5MY95, Q5NVF6, Q5RFQ8, Q62994, Q63148, Q6IY74, Q8BH73, Q8HYJ3, Q8HYJ4, Q8HYJ5, Q8HYJ7, Q8HZR3, Q8K1S1, Q8N135, Q923W9, Q9BZG2, Q9H3T2

Diamond homologs: B0S5N4, B2RXS4, D3ZLH5, D3ZPX4, O15031, O43157, O60486, O75051, P51805, P70206, P70207, P70208, Q3UH93, Q6BEA0, Q80UG2, Q8CJH3, Q9HCM2, Q9NTN9, Q9QY40, Q9QZC2, Q9UIW2, Q9ULL4, Q9V4A7, Q9WUH7, Q9Y4D7, Q09YN5, Q80ZA4, Q60519, Q9P283, O42236, Q13591, Q9C0C4, Q62190, Q626H5, Q9H2E6, O95754, Q64151, Q9Z123, Q9Z143, Q90665

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
SEMA5A	“up-regulates activity”	PLXNB3	binding
PLXNB3	“up-regulates activity”	FSCN1
PLXNB3	“up-regulates activity”	ARHGDIA	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	313
Likely benign	57
Benign	21

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
3245014	NC_000023.10:g.(?152482081)(153416424_?)del	Pathogenic
625802	GRCh37/hg19 Xq28(chrX:152980470-153032459)	Pathogenic

SpliceAI

5393 predictions. Top by Δscore:

Variant	Effect	Δscore
X:153767914:G:GG	donor_gain	1.0000
X:153768217:C:CA	acceptor_gain	1.0000
X:153768218:G:A	acceptor_gain	1.0000
X:153768244:CGTA:C	acceptor_loss	1.0000
X:153768245:GTA:G	acceptor_loss	1.0000
X:153768246:TAGG:T	acceptor_loss	1.0000
X:153768247:A:AT	acceptor_loss	1.0000
X:153768247:AG:A	acceptor_gain	1.0000
X:153768248:G:A	acceptor_loss	1.0000
X:153768248:GG:G	acceptor_gain	1.0000
X:153768248:GGATT:G	acceptor_gain	1.0000
X:153768424:ACAAG:A	donor_loss	1.0000
X:153768426:AAGG:A	donor_loss	1.0000
X:153768427:AGGTG:A	donor_loss	1.0000
X:153768429:GTGA:G	donor_loss	1.0000
X:153768430:T:A	donor_loss	1.0000
X:153769072:ACCAG:A	donor_loss	1.0000
X:153769075:AG:A	donor_loss	1.0000
X:153769076:GG:G	donor_loss	1.0000
X:153769077:GT:G	donor_loss	1.0000
X:153769078:T:G	donor_loss	1.0000
X:153769151:T:A	acceptor_gain	1.0000
X:153769803:GCAGG:G	acceptor_loss	1.0000
X:153769804:CA:C	acceptor_loss	1.0000
X:153769806:GGT:G	acceptor_gain	1.0000
X:153769935:GCCAG:G	donor_gain	1.0000
X:153769936:CCAGG:C	donor_loss	1.0000
X:153769937:CAGGT:C	donor_loss	1.0000
X:153769938:AGGT:A	donor_loss	1.0000
X:153769939:GGT:G	donor_loss	1.0000

AlphaMissense

12317 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:153774800:T:C	F1309L	0.998
X:153774802:C:A	F1309L	0.998
X:153774802:C:G	F1309L	0.998
X:153774883:T:C	L1312P	0.998
X:153774280:T:C	L1205P	0.997
X:153777370:T:C	L1697P	0.997
X:153777535:T:C	L1703P	0.997
X:153773907:A:C	S1110R	0.996
X:153773909:C:A	S1110R	0.996
X:153773909:C:G	S1110R	0.996
X:153774801:T:C	F1309S	0.996
X:153777380:G:C	K1700N	0.996
X:153777380:G:T	K1700N	0.996
X:153777675:T:A	W1750R	0.996
X:153777675:T:C	W1750R	0.996
X:153772277:T:G	F922C	0.995
X:153767896:T:A	C357S	0.994
X:153767897:G:C	C357S	0.994
X:153774249:T:C	C1195R	0.994
X:153774286:G:A	C1207Y	0.994
X:153774801:T:G	F1309C	0.994
X:153767824:T:A	C333S	0.993
X:153767825:G:C	C333S	0.993
X:153773400:T:G	F1026C	0.993
X:153774249:T:A	C1195S	0.993
X:153774250:G:C	C1195S	0.993
X:153774287:C:G	C1207W	0.993
X:153776358:T:A	W1578R	0.993
X:153776358:T:C	W1578R	0.993
X:153776888:T:A	V1612D	0.993

dbSNP variants (sampled 300 via entrez): RS1000553617 (X:153766110 C>G,T), RS1000652835 (X:153770740 G>A,C), RS1000728365 (X:153775267 G>A), RS1001444808 (X:153773196 G>A,C), RS1001497275 (X:153773050 G>A,T), RS1001521011 (X:153779417 T>G), RS1001790367 (X:153768777 G>C), RS1002088348 (X:153765201 C>T), RS1002380065 (X:153769687 C>G,T), RS1003118185 (X:153772103 G>A,C), RS1003761237 (X:153763652 A>G), RS1003955955 (X:153778045 G>A), RS1004968259 (X:153779454 G>A), RS1004978879 (X:153763959 T>C), RS1005552400 (X:153771293 C>G)

Disease associations

OMIM: gene MIM:300214 | disease phenotypes: MIM:300673, MIM:300475, MIM:300100

GenCC curated gene-disease

Mondo (5): severe neonatal-onset encephalopathy with microcephaly (MONDO:0010397), autism spectrum disorder (MONDO:0005258), severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (MONDO:0010334), adrenoleukodystrophy (MONDO:0018544), neurodevelopmental disorder (MONDO:0700092)

Orphanet (5): MECP2-related severe neonatal encephalopathy (Orphanet:209370), Severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome (Orphanet:369939), CADDS (Orphanet:369942), X-linked adrenoleukodystrophy (Orphanet:43), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (4)

Descriptor	Name	Tree numbers
D000326	Adrenoleukodystrophy	C10.228.140.163.100.084; C10.228.140.163.100.362.250; C10.228.140.695.625.250; C10.314.400.250; C10.597.606.360.455.124; C16.320.322.500.124; C16.320.400.525.124; C16.320.565.189.084; C16.320.565.189.362.250; C16.320.565.663.100; C18.452.132.100.084; C18.452.132.100.362.250; C18.452.648.189.084; C18.452.648.189.362.250; C18.452.648.663.100; C19.053.500.270
D065886	Neurodevelopmental Disorders	F03.625
C564508	Contiguous Abcd1-Dxs1375e Deletion Syndrome (supp.)
C566878	Encephalopathy, Neonatal Severe, Due To Mecp2 Mutations (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs4898439	PLXNB3		0.00	0

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases expression, affects methylation	3
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Calcitriol	increases expression	1
Cannabidiol	decreases expression	1
Chelating Agents	affects binding, decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Hydrogen Peroxide	increases expression	1
Smoke	decreases expression	1
Dronabinol	increases expression	1
Tobacco Smoke Pollution	affects expression	1
Triclosan	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases expression	1
Okadaic Acid	increases expression	1
Acrylamide	decreases expression	1
S-Nitrosoglutathione	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A5K4	SEES3-1V human PLXNB3, clone1	Embryonic stem cell	Male
CVCL_A5K5	SEES3-1V human PLXNB3, clone2	Embryonic stem cell	Male
CVCL_A5K6	SEES3-1V human PLXNB3, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT01302964	PHASE3	COMPLETED	Mirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523	PHASE3	TERMINATED	Open Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798	PHASE3	COMPLETED	Treatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074	PHASE3	COMPLETED	Behavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749	PHASE3	COMPLETED	A Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922	PHASE3	COMPLETED	Treatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917	PHASE3	TERMINATED	A Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875	PHASE3	TERMINATED	Memantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156	PHASE3	COMPLETED	Modulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153	PHASE3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166	PHASE3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502	PHASE3	WITHDRAWN	Efficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756	PHASE3	COMPLETED	Open-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder
NCT04623398	PHASE3	COMPLETED	Effect of Lithium in Patients With Autism Spectrum Disorder and Phelan-McDermid Syndrome (SHANK3 Haploinsufficiency)
NCT04725383	PHASE3	TERMINATED	Amitriptyline for Repetitive Behaviors in Autism Spectrum Disorders
NCT05212493	PHASE3	COMPLETED	The Effects of Medical Cannabis in Children With Autistic Spectrum Disorder
NCT05361707	PHASE3	UNKNOWN	Evaluating the Effects of Tasimelteon in Individuals With Autism Spectrum Disorder (ASD) and Sleep Disturbances
NCT05439616	PHASE3	COMPLETED	Study of Cariprazine Oral Capsules or Solution to Assess Adverse Events and Change in Irritability Due to Autism Spectrum Disorder (ASD) in Participants Aged 5-17 Years With ASD
NCT06229210	PHASE3	RECRUITING	Safety and Tolerability Trial of Lumateperone in Pediatric Patients With Schizophrenia, Bipolar Disorder or Autism Spectrum Disorder