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PLXNA3 plexin A3 [ Homo sapiens (human) ]

Gene ID: 55558, updated on 11-Jun-2025
Official Symbol
PLXNA3provided by HGNC
Official Full Name
plexin A3provided by HGNC
Primary source
HGNC:HGNC:9101
See related
Ensembl:ENSG00000130827 MIM:300022; AllianceGenome:HGNC:9101
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
6.3; PLXN3; PLXN4; XAP-6; HSSEXGENE
Summary
This gene encodes a member of the plexin class of proteins. The encoded protein is a class 3 semaphorin receptor, and may be involved in cytoskeletal remodeling and as well as apoptosis. Studies of a similar gene in zebrafish suggest that it is important for axon pathfinding in the developing nervous system. This gene may be associated with tumor progression. [provided by RefSeq, Aug 2013]
Expression
Ubiquitous expression in skin (RPKM 7.2), ovary (RPKM 7.2) and 25 other tissues See more
Orthologs
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See PLXNA3 in Genome Data Viewer
Location:
Xq28
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154458281..154477779)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152694791..152714288)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153686621..153706118)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153665032-153665532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153666887-153667386 Neighboring gene GDP dissociation inhibitor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153672115-153672682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153673251-153673818 Neighboring gene family with sequence similarity 50 member A Neighboring gene microRNA 6858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153687524-153688076 Neighboring gene Sharpr-MPRA regulatory region 3405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21109 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153707495-153707994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30063 Neighboring gene L antigen family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153713643-153714401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153714402-153715160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30064 Neighboring gene ubiquitin like 4A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21112 Neighboring gene solute carrier family 10 member 3

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Semaphorin-Plexin Signaling: From Axonal Guidance to a New X-Linked Intellectual Disability Syndrome. Steele JL, et al. Pediatr Neurol, 2022 Jan. PMID 34740135
  2. PLXNA3 Variant rs5945430 is Associated with Severe Clinical Course in Male Multiple Sclerosis Patients. Qureshi M, et al. Neuromolecular Med, 2017 Sep. PMID 28536997
  3. Myeloid translocation gene 16b is a dual A-kinase anchoring protein that interacts selectively with plexins in a phospho-regulated manner. Fiedler SE, et al. FEBS Lett, 2010 Mar 5. PMID 20138877
  4. Identification of plexin family molecules in mice. Kameyama T, et al. Biochem Biophys Res Commun, 1996 Sep 13. PMID 8806646
  5. Semaphorin-plexin signalling genes associated with human breast tumourigenesis. Gabrovska PN, et al. Gene, 2011 Dec 10. PMID 21925246

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Semaphorin-Plexin Signaling: From Axonal Guidance to a New X-Linked Intellectual Disability Syndrome.
    Title: Semaphorin-Plexin Signaling: From Axonal Guidance to a New X-Linked Intellectual Disability Syndrome.
  2. Exome analysis of Kuwaiti multiple sclerosis patients revealed a missense variant (rs5945430) in Plexin A3 (PLXNA3) gene (Xq28) associated with male-specific MS severity and disability.
    Title: PLXNA3 Variant rs5945430 is Associated with Severe Clinical Course in Male Multiple Sclerosis Patients.
  3. Data indicate that plexin A1-4 (PLXNA1-4) mediation of neuroanatomical traits can be detected using in vivo neuroimaging techniques.
    Title: PlexinA polymorphisms mediate the developmental trajectory of human corpus callosum microstructure.
  4. in vitro analysis on PLXNA3 also suggest that this gene may have some form of growth suppressive role in breast cancer, in addition to a similar role for the gene previously reported in ovarian cancer.
    Title: Semaphorin-plexin signalling genes associated with human breast tumourigenesis.
  5. Data show that the expression of Sema3A receptors (neuropilin-1 (NRP-1), NRP-2, plexin A1, plexin A2, and plexin A3) significantly increased during M-CSF-mediated differentiation of monocytes into macrophages.
    Title: Expression and function of semaphorin 3A and its receptors in human monocyte-derived macrophages.
Submit: New GeneRIF Correction

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables semaphorin receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables semaphorin receptor activity IEA
Inferred from Electronic Annotation
more info
  
enables semaphorin receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables signaling receptor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in axon extension IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of axon extension involved in axon guidance IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within axon guidance IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in branchiomotor neuron axon guidance IEA
Inferred from Electronic Annotation
more info
  
involved_in branchiomotor neuron axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell surface receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in facial nerve structural organization IEA
Inferred from Electronic Annotation
more info
  
involved_in facial nerve structural organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within hippocampus development IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within hippocampus development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in motor neuron axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within negative chemotaxis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative chemotaxis IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within neuron projection extension IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within neuron projection guidance IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within neuron projection guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in olfactory nerve formation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within pyramidal neuron development IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within pyramidal neuron development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of axon extension involved in axon guidance IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of axonogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of chemotaxis IEA
Inferred from Electronic Annotation
more info
  
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in semaphorin-plexin signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in semaphorin-plexin signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in semaphorin-plexin signaling pathway NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in telencephalon development IEA
Inferred from Electronic Annotation
more info
  
involved_in trigeminal nerve structural organization IEA
Inferred from Electronic Annotation
more info
  
involved_in trigeminal nerve structural organization ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
part_of semaphorin receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of semaphorin receptor complex TAS
Traceable Author Statement
more info
 PubMed 
Preferred Names
plexin-A3
Names
Sex chromosome X transmembrane protein of HGF receptor family 3
plexin-4
semaphorin receptor SEX

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_021298.2 RefSeqGene

    Range
    5007..20372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_017514.5 → NP_059984.3  plexin-A3 precursor

    Status: REVIEWED

    Source sequence(s)
    AC244090, AW001914, BF798844, BG820285, BQ718472, BQ720233, CN427844, CN484803, HY098587, HY158513, X87852
    Consensus CDS
    CCDS14752.1
    UniProtKB/Swiss-Prot
    P51805, Q5HY36
    Related
    ENSP00000358696.3, ENST00000369682.4
    Conserved Domains (8) summary
    cd11273
    Location:21 → 489
    Sema_plexin_A3; The Sema domain, a protein interacting module, of Plexin A3
    smart00423
    Location:788 → 831
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd00603
    Location:1125 → 1208
    IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
    cd01179
    Location:935 → 1021
    IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01180
    Location:840 → 934
    IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    cd01181
    Location:1023 → 1123
    IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...
    pfam01437
    Location:490 → 530
    PSI; Plexin repeat
    pfam08337
    Location:1294 → 1841
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    154458281..154477779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442247.1 → XP_047298203.1  plexin-A3 isoform X1

RNA

  1. XR_007068193.1 RNA Sequence

  2. XR_430556.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152694791..152714288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327369.1 → XP_054183344.1  plexin-A3 isoform X1

RNA

  1. XR_008485494.1 RNA Sequence

  2. XR_008485493.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51805.3 GenPept UniProtKB/Swiss-Prot:P51805

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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