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PLXNC1 plexin C1 [ Homo sapiens (human) ]

Gene ID: 10154, updated on 11-Apr-2024

Summary

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Official Symbol
PLXNC1provided by HGNC
Official Full Name
plexin C1provided by HGNC
Primary source
HGNC:HGNC:9106
See related
Ensembl:ENSG00000136040 MIM:604259; AllianceGenome:HGNC:9106
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
CD232; VESPR; PLXN-C1
Summary
This gene encodes a member of the plexin family. Plexins are transmembrane receptors for semaphorins, a large family of proteins that regulate axon guidance, cell motility and migration, and the immune response. The encoded protein and its ligand regulate melanocyte adhesion, and viral semaphorins may modulate the immune response by binding to this receptor. The encoded protein may be a tumor suppressor protein for melanoma. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jan 2011]
Expression
Broad expression in appendix (RPKM 8.1), testis (RPKM 6.6) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
12q22
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (94148577..94307675)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (94129732..94288500)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (94542353..94701451)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6774 Neighboring gene uncharacterized LOC124902986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4720 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6778 Neighboring gene REST corepressor 2 pseudogene Neighboring gene uncharacterized LOC124902988 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:94563164-94563859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:94564987-94565496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:94579005-94579506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:94580673-94581173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6782 Neighboring gene uncharacterized LOC124902987 Neighboring gene MPRA-validated peak1895 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:94654721-94655463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4726 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94657254-94658018 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94658019-94658782 Neighboring gene centrosomal protein 83 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94698110-94698989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4727 Neighboring gene RNA, 7SL, cytoplasmic 330, pseudogene Neighboring gene RNA binding motif single stranded interacting protein 2 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The Relationship Between Plexin C1 Overexpression and Survival in Hepatocellular Carcinoma: a Turkish Oncology Group (TOG) Study. NazimTurhal S, et al. J Gastrointest Cancer, 2022 Jun. PMID 33656690
  2. Mechanical tension alters semaphorin expression in the periodontium. Spencer AY, et al. J Periodontol, 2009 Oct. PMID 19792857
  3. Molecular profiling of the "plexinome" in melanoma and pancreatic cancer. Balakrishnan A, et al. Hum Mutat, 2009 Aug. PMID 19462467, Free PMC Article
  4. Identification of genes with abnormal expression changes in acute myeloid leukemia. Stirewalt DL, et al. Genes Chromosomes Cancer, 2008 Jan. PMID 17910043
  5. Soluble CD100 functions on human monocytes and immature dendritic cells require plexin C1 and plexin B1, respectively. Chabbert-de Ponnat I, et al. Int Immunol, 2005 Apr. PMID 15746246

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PLXNC1 interference alleviates the inflammatory injury, apoptosis and extracellular matrix degradation of IL-1beta-exposed chondrocytes via suppressing GRP78 expression.
    Title: PLXNC1 interference alleviates the inflammatory injury, apoptosis and extracellular matrix degradation of IL-1β-exposed chondrocytes via suppressing GRP78 expression.
  2. The Relationship Between Plexin C1 Overexpression and Survival in Hepatocellular Carcinoma: a Turkish Oncology Group (TOG) Study.
    Title: The Relationship Between Plexin C1 Overexpression and Survival in Hepatocellular Carcinoma: a Turkish Oncology Group (TOG) Study.
  3. Results indicated that PLXNC1 was a direct target of miR-4500. Its knockdown inhibits proliferation and invasion of papillary thyroid cancer (PTC) cells. On the contrary, its overexpression of impairs miR-4500-induced inhibition of PTC malignancy.
    Title: MiR-4500 Regulates PLXNC1 and Inhibits Papillary Thyroid Cancer Progression.
  4. Results indicate that long non-coding RNA (lncRNA) CASC2 can promote PLXNC1 expression by sponging miR-181a, thereby inhibiting the proliferation and invasion of melanoma cells.
    Title: Long non-coding RNA CASC2 inhibits tumorigenesis via the miR-181a/PLXNC1 axis in melanoma.
  5. Plexin C1 deficiency permits synaptotagmin 7-mediated macrophage migration and enhances mammalian lung fibrosis
    Title: Plexin C1 deficiency permits synaptotagmin 7-mediated macrophage migration and enhances mammalian lung fibrosis.
  6. loss of Plexin C1 in melanoma may promote early steps in melanoma progression through suppression of migration and proliferation
    Title: The neural guidance receptor Plexin C1 delays melanoma progression.
  7. Study reports the structures of Sema7A and A39R complexed with the Semaphorin-binding module of PlexinC1; both structures show two PlexinC1 molecules symmetrically bridged by Semaphorin dimers.
    Title: Structural basis of semaphorin-plexin recognition and viral mimicry from Sema7A and A39R complexes with PlexinC1.
  8. significant loss of Plexin C1 in metastatic melanoma compared with primary melanoma, suggesting the possibility that the Plexin C1 receptor is a tumor suppressor protein for melanoma
    Title: The semaphorin 7A receptor Plexin C1 is lost during melanoma metastasis.
  9. Plexin C1, a receptor for semaphorin 7a, inactivates cofilin and is a potential tumor suppressor for melanoma progression.
    Title: Plexin C1, a receptor for semaphorin 7a, inactivates cofilin and is a potential tumor suppressor for melanoma progression.
  10. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Neither replication nor simulation supports a role for the axon guidance pathway in the genetics of Parkinson's disease.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide scan for breast cancer risk haplotypes among African American women.
EBI GWAS Catalog
TSPYL5 SNPs: association with plasma estradiol concentrations and aromatase expression.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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 signaling receptor binding TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell adhesion TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of axonogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cell shape IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of synapse pruning IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cerebellar climbing fiber to Purkinje cell synapse IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
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
  

General protein information

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Preferred Names
plexin-C1
Names
plexin (semaphorin receptor)
receptor for viral semaphorin protein
receptor for virally-encoded semaphorin
virus-encoded semaphorin protein receptor

NCBI Reference Sequences (RefSeq)

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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_050648.2 RefSeqGene

    Range
    5002..164100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005761.3 → NP_005752.1  plexin-C1 precursor

    See identical proteins and their annotated locations for NP_005752.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the functional protein.
    Source sequence(s)
    AC073655, AC123567
    Consensus CDS
    CCDS9049.1
    UniProtKB/Swiss-Prot
    O60486, Q59H25
    Related
    ENSP00000258526.4, ENST00000258526.9
    Conserved Domains (6) summary
    cd11246
    Location:44 → 453
    Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
    smart00423
    Location:591 → 635
    PSI; domain found in Plexins, Semaphorins and Integrins
    smart00429
    Location:753 → 841
    IPT; ig-like, plexins, transcription factors
    pfam01437
    Location:454 → 507
    PSI; Plexin repeat
    pfam01833
    Location:664 → 750
    TIG; IPT/TIG domain
    pfam08337
    Location:1012 → 1535
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain

RNA

  1. NR_037687.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks multiple 5' exons but contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest in-frame ORF. Translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC073655

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    94148577..94307675
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719186.5 → XP_006719249.1  plexin-C1 isoform X1

    Conserved Domains (6) summary
    cd11246
    Location:44 → 453
    Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
    smart00423
    Location:591 → 635
    PSI; domain found in Plexins, Semaphorins and Integrins
    smart00429
    Location:753 → 841
    IPT; ig-like, plexins, transcription factors
    pfam01437
    Location:454 → 507
    PSI; Plexin repeat
    pfam01833
    Location:664 → 750
    TIG; IPT/TIG domain
    pfam08337
    Location:1012 → 1522
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain

  2. XM_047428050.1 → XP_047284006.1  plexin-C1 isoform X2

  3. XM_011537730.4 → XP_011536032.1  plexin-C1 isoform X3

    Conserved Domains (6) summary
    cd11246
    Location:44 → 453
    Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
    smart00423
    Location:591 → 635
    PSI; domain found in Plexins, Semaphorins and Integrins
    smart00429
    Location:753 → 841
    IPT; ig-like, plexins, transcription factors
    pfam01437
    Location:454 → 507
    PSI; Plexin repeat
    pfam01833
    Location:664 → 750
    TIG; IPT/TIG domain
    pfam08337
    Location:1012 → 1292
    Plexin_cytopl; Plexin cytoplasmic RasGAP domain

  4. XM_011537731.4 → XP_011536033.1  plexin-C1 isoform X4

    Conserved Domains (6) summary
    cd11246
    Location:44 → 453
    Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
    smart00423
    Location:591 → 635
    PSI; domain found in Plexins, Semaphorins and Integrins
    smart00429
    Location:753 → 841
    IPT; ig-like, plexins, transcription factors
    pfam01437
    Location:454 → 507
    PSI; Plexin repeat
    pfam01833
    Location:664 → 750
    TIG; IPT/TIG domain
    cl02569
    Location:1010 → 1029
    RasGAP; Ras GTPase Activating Domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    94129732..94288500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370727.1 → XP_054226702.1  plexin-C1 isoform X1

  2. XM_054370728.1 → XP_054226703.1  plexin-C1 isoform X2

  3. XM_054370729.1 → XP_054226704.1  plexin-C1 isoform X3

  4. XM_054370730.1 → XP_054226705.1  plexin-C1 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60486.1 GenPept UniProtKB/Swiss-Prot:O60486

Gene LinkOut

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