PLXNC1 plexin C1 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 12q22

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (94148577..94307675)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (94129732..94288500)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (94542353..94701451)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Semaphorin 7A promotes endothelial permeability and inflammation via plexin C1 and integrin beta1 in Kawasaki disease.
Title: Semaphorin 7A promotes endothelial permeability and inflammation via plexin C1 and integrin β1 in Kawasaki disease.
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.
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.
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.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (12)

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 EBI GWAS CatalogPubMed
TSPYL5 SNPs: association with plasma estradiol concentrations and aromatase expression. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D12S829 (e-PCR)
- UniSTS:149266

RH120803 (e-PCR)
- UniSTS:132884

SHGC-85070 (e-PCR)
- UniSTS:103452

RH46103 (e-PCR)
- UniSTS:46108

G64441 (e-PCR)
- UniSTS:163673

G64528 (e-PCR)
- UniSTS:163677

RH123168 (e-PCR)
- UniSTS:135549

G64440 (e-PCR)
- UniSTS:163981

RH45721 (e-PCR)
- UniSTS:53902

WI-14237 (e-PCR)
- UniSTS:11724

D12S2125 (e-PCR)
- UniSTS:39884

RH91966 (e-PCR)
- UniSTS:86230

RH68932 (e-PCR)
- UniSTS:54772

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 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
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse assembly	IBA Inferred from Biological aspect of Ancestor 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 more info	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

NG_050648.2 RefSeqGene

Range

5002..164100

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

94148577..94307675

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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