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... See more...

Aliases for PLXNC1 Gene

Aliases for PLXNC1 Gene

  • Plexin C1 2 3 5
  • Virus-Encoded Semaphorin Protein Receptor 3 4
  • Plexin-C1 3 4
  • VESPR 3 4
  • Receptor For Virally-Encoded Semaphorin 3
  • Receptor For Viral Semaphorin Protein 3
  • Plexin (Semaphorin Receptor) 3
  • CD232 Antigen 4
  • PLXN-C1 3
  • CD232 3

External Ids for PLXNC1 Gene

Previous GeneCards Identifiers for PLXNC1 Gene

  • GC12P094074
  • GC12P095063
  • GC12P094475
  • GC12P093044
  • GC12P093066
  • GC12P094542
  • GC12P091610

Summaries for PLXNC1 Gene

Entrez Gene Summary for PLXNC1 Gene

  • 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]

GeneCards Summary for PLXNC1 Gene

PLXNC1 (Plexin C1) is a Protein Coding gene. Diseases associated with PLXNC1 include Polycystic Kidney Disease 4 With Or Without Polycystic Liver Disease. Among its related pathways are Developmental Biology and Semaphorin interactions. Gene Ontology (GO) annotations related to this gene include signaling receptor binding. An important paralog of this gene is PLXND1.

UniProtKB/Swiss-Prot Summary for PLXNC1 Gene

  • Receptor for SEMA7A, for smallpox semaphorin A39R, vaccinia virus semaphorin A39R and for herpesvirus Sema protein. Binding of semaphorins triggers cellular responses leading to the rearrangement of the cytoskeleton and to secretion of IL6 and IL8 (By similarity).

Additional gene information for PLXNC1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PLXNC1 Gene

Genomics for PLXNC1 Gene

GeneHancer (GH) Regulatory Elements for PLXNC1 Gene

Promoters and enhancers for PLXNC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J094147 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 783.6 +1.8 1762 6.3 FOXA1 HDAC2 NR2F1 NR2F6 MIXL1 HLF RAD21 ZNF652 CTCF RERE PLXNC1 TMCC3 RN7SL737P CRADD ENSG00000258035
GH12J094260 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 784.6 +115.9 115939 8 SP1 HCFC1 MYC ETV6 RELA L3MBTL2 MAX POU5F1 ZNF148 NKRF PLXNC1 TMCC3 ENSG00000258172 ENSG00000258365 ENSG00000257252 ENSG00000287237 CEP83
GH12J094171 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 50.3 +24.8 24824 3.7 ZBTB40 LCORL ATF1 CREB1 MIXL1 MYC ETV6 RELA HLF L3MBTL2 PLXNC1 TMCC3 ENSG00000258035
GH12J094643 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 37.9 +495.9 495920 1.9 SP1 SP7 ZSCAN21 IKZF1 RXRA ZEB2 ZNF629 SCRT2 ZNF10 OSR2 HSALNG0093197 TMCC3 PLXNC1 lnc-CEP83-4
GH12J094239 Enhancer 1.2 FANTOM5 Ensembl ENCODE 30.6 +95.2 95187 8.5 ZNF24 SP1 SMARCE1 MYC RELA MAX NFIB ZFX MLLT1 ZNF687 PLXNC1 TMCC3 SOCS2 UBE2N ENSG00000287237 ENSG00000258035
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLXNC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PLXNC1 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • GATA-2
  • Pax-5
  • Spz1

Genomic Locations for PLXNC1 Gene

Genomic Locations for PLXNC1 Gene
chr12:94,148,577-94,307,675
(GRCh38/hg38)
Size:
159,099 bases
Orientation:
Plus strand
chr12:94,542,499-94,701,451
(GRCh37/hg19)
Size:
158,953 bases
Orientation:
Plus strand

Genomic View for PLXNC1 Gene

Genes around PLXNC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLXNC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLXNC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLXNC1 Gene

Proteins for PLXNC1 Gene

  • Protein details for PLXNC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60486-PLXC1_HUMAN
    Recommended name:
    Plexin-C1
    Protein Accession:
    O60486
    Secondary Accessions:
    • Q59H25

    Protein attributes for PLXNC1 Gene

    Size:
    1568 amino acids
    Molecular mass:
    175742 Da
    Quaternary structure:
    • Monomer. Homodimer. Interacts with SEMA7A.

    Three dimensional structures from OCA and Proteopedia for PLXNC1 Gene

neXtProt entry for PLXNC1 Gene

Post-translational modifications for PLXNC1 Gene

  • N-glycosylated.
  • Glycosylation at Asn86, Asn141, Asn149, Asn241, Asn252, Asn386, Asn407, Asn548, Asn582, Asn653, Asn686, Asn692, Asn771, Asn796, Asn821, Asn871, and Asn890
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PLXC1_HUMAN (725)

No data available for DME Specific Peptides for PLXNC1 Gene

Domains & Families for PLXNC1 Gene

Gene Families for PLXNC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • CD markers
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for PLXNC1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60256, highly similar to Plexin-C1 (B4DHQ7_HUMAN)
  • Virus-encoded semaphorin protein receptor (PLXC1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O60486

UniProtKB/Swiss-Prot:

PLXC1_HUMAN :
  • Belongs to the plexin family.
Family:
  • Belongs to the plexin family.
genes like me logo Genes that share domains with PLXNC1: view

Function for PLXNC1 Gene

Molecular function for PLXNC1 Gene

UniProtKB/Swiss-Prot Function:
Receptor for SEMA7A, for smallpox semaphorin A39R, vaccinia virus semaphorin A39R and for herpesvirus Sema protein. Binding of semaphorins triggers cellular responses leading to the rearrangement of the cytoskeleton and to secretion of IL6 and IL8 (By similarity).
GENATLAS Biochemistry:
plexin C1,calcium-dependent cell adhesion molecule at the neuronal cell surface,receptor for the semaphorin 7A (SEMA7A)

Phenotypes From GWAS Catalog for PLXNC1 Gene

Gene Ontology (GO) - Molecular Function for PLXNC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding TAS 9586637
GO:0005515 protein binding IPI,IEA 20727575
GO:0017154 semaphorin receptor activity IEA,IBA 21873635
genes like me logo Genes that share ontologies with PLXNC1: view
genes like me logo Genes that share phenotypes with PLXNC1: view

Animal Models for PLXNC1 Gene

MGI Knock Outs for PLXNC1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLXNC1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLXNC1 Gene

Localization for PLXNC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLXNC1 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PLXNC1 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
peroxisome 1
mitochondrion 0
cytosol 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PLXNC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002116 semaphorin receptor complex IBA 21873635
GO:0005886 plasma membrane TAS,NAS --
GO:0005887 integral component of plasma membrane IBA 21873635
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PLXNC1: view

Pathways & Interactions for PLXNC1 Gene

genes like me logo Genes that share pathways with PLXNC1: view

Pathways by source for PLXNC1 Gene

1 KEGG pathway for PLXNC1 Gene

SIGNOR curated interactions for PLXNC1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for PLXNC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 9586637
GO:0007162 negative regulation of cell adhesion IBA 21873635
GO:0007165 signal transduction IEA --
GO:0008360 regulation of cell shape IBA 21873635
GO:0030334 regulation of cell migration IBA 21873635
genes like me logo Genes that share ontologies with PLXNC1: view

Drugs & Compounds for PLXNC1 Gene

(4) Drugs for PLXNC1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for PLXNC1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PLXNC1: view

Transcripts for PLXNC1 Gene

mRNA/cDNA for PLXNC1 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLXNC1

Alternative Splicing Database (ASD) splice patterns (SP) for PLXNC1 Gene

No ASD Table

Relevant External Links for PLXNC1 Gene

GeneLoc Exon Structure for
PLXNC1
ECgene alternative splicing isoforms for
PLXNC1

Expression for PLXNC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PLXNC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PLXNC1 Gene

This gene is overexpressed in Whole Blood (x17.8).

Protein differential expression in normal tissues from HIPED for PLXNC1 Gene

This gene is overexpressed in Fetal Brain (20.6) and Neutrophil (13.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PLXNC1 Gene



Protein tissue co-expression partners for PLXNC1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PLXNC1 Gene:

PLXNC1

SOURCE GeneReport for Unigene cluster for PLXNC1 Gene:

Hs.584845

mRNA Expression by UniProt/SwissProt for PLXNC1 Gene:

O60486-PLXC1_HUMAN
Tissue specificity: Detected in heart, brain, lung, spleen and placenta.

Evidence on tissue expression from TISSUES for PLXNC1 Gene

  • Nervous system(4.7)
  • Skin(2.3)
  • Blood(2)
genes like me logo Genes that share expression patterns with PLXNC1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PLXNC1 Gene

Orthologs for PLXNC1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PLXNC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLXNC1 33 32
  • 99.66 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 33
  • 93 (a)
OneToMany
-- 33
  • 66 (a)
OneToMany
-- 33
  • 18 (a)
OneToMany
dog
(Canis familiaris)
Mammalia PLXNC1 33 32
  • 91.23 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PLXNC1 33 32
  • 90.11 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Plxnc1 17 33 32
  • 87.73 (n)
rat
(Rattus norvegicus)
Mammalia Plxnc1 32
  • 86.64 (n)
oppossum
(Monodelphis domestica)
Mammalia PLXNC1 33
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLXNC1 33 32
  • 66.81 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLXNC1 33
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plxnc1 32
  • 53.75 (n)
Str.17344 32
zebrafish
(Danio rerio)
Actinopterygii plxnc1 33 32
  • 52.29 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9975 32
sea squirt
(Ciona savignyi)
Ascidiacea Cin.10318 32
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.10318 32
Species where no ortholog for PLXNC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PLXNC1 Gene

ENSEMBL:
Gene Tree for PLXNC1 (if available)
TreeFam:
Gene Tree for PLXNC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLXNC1: view image

Paralogs for PLXNC1 Gene

Paralogs for PLXNC1 Gene

(17) SIMAP similar genes for PLXNC1 Gene using alignment to 6 proteins:

  • PLXC1_HUMAN
  • B4DHQ7_HUMAN
  • F5H3A2_HUMAN
  • F8VUW4_HUMAN
  • F8W095_HUMAN
  • F8W1K6_HUMAN
genes like me logo Genes that share paralogs with PLXNC1: view

Variants for PLXNC1 Gene

Sequence variations from dbSNP and Humsavar for PLXNC1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs146747324 likely-benign, Anophthalmia - microphthalmia 94,279,523(+) T/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs115408156 likely-benign, not provided 94,298,702(+) T/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1555208581 uncertain-significance, not provided 94,282,405(+) A/G genic_downstream_transcript_variant, intron_variant
rs1000004509 -- 94,293,142(+) A/T genic_downstream_transcript_variant, intron_variant
rs1000013022 -- 94,276,830(+) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PLXNC1 Gene

Variant ID Type Subtype PubMed ID
dgv2793n54 CNV loss 21841781
dgv2794n54 CNV loss 21841781
dgv2795n54 CNV loss 21841781
dgv2796n54 CNV loss 21841781
dgv2797n54 CNV loss 21841781
dgv853n106 CNV deletion 24896259
esv2663356 CNV deletion 23128226
esv2746225 CNV deletion 23290073
esv2746226 CNV deletion 23290073
esv29104 CNV loss 19812545
esv3549597 CNV deletion 23714750
esv3549602 CNV deletion 23714750
esv3630416 CNV loss 21293372
esv4528 CNV loss 18987735
nsv1071047 CNV deletion 25765185
nsv1118242 CNV deletion 24896259
nsv437769 CNV loss 16327808
nsv519828 CNV loss 19592680
nsv520739 CNV loss 19592680
nsv53225 CNV deletion 16902084
nsv559794 CNV gain 21841781
nsv559802 CNV gain 21841781
nsv7234 OTHER inversion 18451855
nsv828 CNV insertion 18451855
nsv832489 CNV loss 17160897
nsv9000 CNV gain 18304495
nsv957917 CNV deletion 24416366

Variation tolerance for PLXNC1 Gene

Residual Variation Intolerance Score: 2.88% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.63; 86.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLXNC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLXNC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLXNC1 Gene

Disorders for PLXNC1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PLXNC1 Gene - From: DISEASES and Novoseek

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PLXNC1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PLXNC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PLXNC1 Gene

Publications for PLXNC1 Gene

  1. A poxvirus-encoded semaphorin induces cytokine production from monocytes and binds to a novel cellular semaphorin receptor, VESPR. (PMID: 9586637) Comeau MR … Spriggs MK (Immunity 1998) 3 4 23 56
  2. Structural basis of semaphorin-plexin recognition and viral mimicry from Sema7A and A39R complexes with PlexinC1. (PMID: 20727575) Liu H … He X (Cell 2010) 3 4 56
  3. Plexin C1, a receptor for semaphorin 7a, inactivates cofilin and is a potential tumor suppressor for melanoma progression. (PMID: 18987670) Scott GA … Fender A (The Journal of investigative dermatology 2009) 3 23 56
  4. Mechanical tension alters semaphorin expression in the periodontium. (PMID: 19792857) Spencer AY … Lallier TE (Journal of periodontology 2009) 3 23 56
  5. The semaphorin 7A receptor Plexin C1 is lost during melanoma metastasis. (PMID: 19318806) Lazova R … Scott G (The American Journal of dermatopathology 2009) 3 23 56

Products for PLXNC1 Gene

Sources for PLXNC1 Gene