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NECTIN1 nectin cell adhesion molecule 1 [ Homo sapiens (human) ]

Gene ID: 5818, updated on 2-Nov-2024

Summary

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Official Symbol
NECTIN1provided by HGNC
Official Full Name
nectin cell adhesion molecule 1provided by HGNC
Primary source
HGNC:HGNC:9706
See related
Ensembl:ENSG00000110400 MIM:600644; AllianceGenome:HGNC:9706
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
ED4; PRR; HIgR; HV1S; HVEC; OFC7; PRR1; PVRR; CD111; PVRL1; PVRR1; SK-12; CLPED1; nectin-1
Summary
This gene encodes an adhesion protein that plays a role in the organization of adherens junctions and tight junctions in epithelial and endothelial cells. The protein is a calcium(2+)-independent cell-cell adhesion molecule that belongs to the immunoglobulin superfamily and has 3 extracellular immunoglobulin-like loops, a single transmembrane domain (in some isoforms), and a cytoplasmic region. This protein acts as a receptor for glycoprotein D (gD) of herpes simplex viruses 1 and 2 (HSV-1, HSV-2), and pseudorabies virus (PRV) and mediates viral entry into epithelial and neuronal cells. Mutations in this gene cause cleft lip and palate/ectodermal dysplasia 1 syndrome (CLPED1) as well as non-syndromic cleft lip with or without cleft palate (CL/P). Alternative splicing results in multiple transcript variants encoding proteins with distinct C-termini. [provided by RefSeq, Oct 2009]
Expression
Biased expression in skin (RPKM 64.2), esophagus (RPKM 38.3) and 8 other tissues See more
Orthologs
mouse all
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Genomic context

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See NECTIN1 in Genome Data Viewer
Location:
11q23.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119638098..119729200, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119660108..119752026, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (119508808..119599910, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902770 Neighboring gene uncharacterized LOC107984398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119456019-119456834 Neighboring gene NANOG hESC enhancer GRCh37_chr11:119484842-119485365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119486841-119487430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119488611-119489198 Neighboring gene keratin 8 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119493452-119494328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119494329-119495203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119498707-119499582 Neighboring gene uncharacterized LOC105369520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119507935-119508436 Neighboring gene uncharacterized LOC124900303 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:119520624-119521191 Neighboring gene RNA, U6 small nuclear 1123, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119535306-119535844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119535845-119536381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5633 Neighboring gene Sharpr-MPRA regulatory region 6199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119560233-119560733 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119562395-119563120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119563121-119563847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119564585-119565134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119565135-119565682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119566971-119567596 Neighboring gene NECTIN1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119584957-119585597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119588639-119589412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119594703-119595203 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:119597492-119598434 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:119599234-119600095 and GRCh37_chr11:119600096-119600956 Neighboring gene NECTIN1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119618498-119618998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119656890-119657713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119657714-119658536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119658954-119659491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119666350-119666971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119680838-119681338 Neighboring gene DExD-box helicase 39B pseudogene

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 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. Access to nectin favors herpes simplex virus infection at the apical surface of polarized human epithelial cells. Galen B, et al. J Virol, 2006 Dec. PMID 17005657, Free PMC Article
  2. Host nectin-1 is required for efficient Chlamydia trachomatis serovar E development. Hall JV, et al. Front Cell Infect Microbiol, 2014. PMID 25414835, Free PMC Article
  3. Herpes B virus gD interaction with its human receptor--an in silico analysis approach. Li L, et al. Theor Biol Med Model, 2014 Jun 6. PMID 24902525, Free PMC Article
  4. Novel insertion mutation in the PVRL1 gene in Turkish patients with non-syndromic cleft lip with/without cleft palate. Aşlar D, et al. Arch Oral Biol, 2014 Mar. PMID 24581844
  5. Increased axonal expression of nectin-1 in multiple sclerosis plaques. Castellanos KJ, et al. Neurol Sci, 2013 Apr. PMID 22460696

See all (108) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic associations and parent-of-origin effects of PVRL1 in non-syndromic cleft lip with or without cleft palate across multiple ethnic populations.
    Title: Genetic associations and parent-of-origin effects of PVRL1 in non-syndromic cleft lip with or without cleft palate across multiple ethnic populations.
  2. Downregulation of endogenous nectin1 in human keratinocytes by herpes simplex virus 1 glycoprotein D excludes superinfection but does not affect NK cell function.
    Title: Downregulation of endogenous nectin1 in human keratinocytes by herpes simplex virus 1 glycoprotein D excludes superinfection but does not affect NK cell function.
  3. Ex Vivo Infection of Human Skin Models with Herpes Simplex Virus 1: Accessibility of the Receptor Nectin-1 during Formation or Impairment of Epidermal Barriers Is Restricted by Tight Junctions.
    Title: Ex Vivo Infection of Human Skin Models with Herpes Simplex Virus 1: Accessibility of the Receptor Nectin-1 during Formation or Impairment of Epidermal Barriers Is Restricted by Tight Junctions.
  4. Loss of NECTIN1 triggers melanoma dissemination upon local IGF1 depletion.
    Title: Loss of NECTIN1 triggers melanoma dissemination upon local IGF1 depletion.
  5. A monoclonal antibody neutralizes pesudorabies virus by blocking gD binding to the receptor nectin-1.
    Title: A monoclonal antibody neutralizes pesudorabies virus by blocking gD binding to the receptor nectin-1.
  6. Hepatocellular Carcinoma Cells Up-regulate PVRL1, Stabilizing PVR and Inhibiting the Cytotoxic T-Cell Response via TIGIT to Mediate Tumor Resistance to PD1 Inhibitors in Mice.
    Title: Hepatocellular Carcinoma Cells Up-regulate PVRL1, Stabilizing PVR and Inhibiting the Cytotoxic T-Cell Response via TIGIT to Mediate Tumor Resistance to PD1 Inhibitors in Mice.
  7. Generation of an Oncolytic Herpes Simplex Viral Vector Completely Retargeted to the GDNF Receptor GFRalpha1 for Specific Infection of Breast Cancer Cells.
    Title: Generation of an Oncolytic Herpes Simplex Viral Vector Completely Retargeted to the GDNF Receptor GFRα1 for Specific Infection of Breast Cancer Cells.
  8. Nectin-1-expressing cells acquire dye-labeled cytoplasmic proteins synchronously with nectin-4, a process most active during cell adhesion.
    Title: Trans-endocytosis elicited by nectins transfers cytoplasmic cargo, including infectious material, between cells.
  9. Nectin-1 directly interacts with CD96 in vitro. The binding site for CD96 is located on the nectin-1 V-domain, which comprises a canonical interface that is shared by nectins to promote cell adhesion. The affinity of nectin-1 for CD96 is lower than for other nectins such as nectin-3 and nectin-1 itself.
    Title: Interaction between nectin-1 and the human natural killer cell receptor CD96.
  10. Brain tumor expression of nectin-1 may be a useful biomarker to predict patient response to oHSV.
    Title: Enhanced Sensitivity of Patient-Derived Pediatric High-Grade Brain Tumor Xenografts to Oncolytic HSV-1 Virotherapy Correlates with Nectin-1 Expression.
Submit: New GeneRIF Correction See all GeneRIFs (57)

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

Associated conditions

Description Tests
Cleft lip/palate-ectodermal dysplasia syndrome
MedGen: C2931488 OMIM: 225060 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of NECTIN1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120-mediated disruption of polarized oral epithelial junctions leads to exposure of nectin-1 and facilitate its binding to HSV-1 PubMed
Tat tat HIV-1 Tat-mediated disruption of polarized oral epithelial junctions leads to exposure of nectin-1 and facilitate its binding to HSV-1 PubMed

Go to the HIV-1, Human Interaction Database

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

Clone Names

  • MGC16207, MGC142031

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
enables cell adhesion molecule binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables coreceptor activity TAS
Traceable Author Statement
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
  
enables virion binding IEA
Inferred from Electronic Annotation
more info
  
enables virus receptor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in axon guidance IEA
Inferred from Electronic Annotation
more info
  
involved_in cell adhesion NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in cell-cell adhesion NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in desmosome organization IEA
Inferred from Electronic Annotation
more info
  
involved_in enamel mineralization IEA
Inferred from Electronic Annotation
more info
  
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in immune response NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in iron ion transport IEA
Inferred from Electronic Annotation
more info
  
involved_in lens morphogenesis in camera-type eye IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization to cell junction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in retina development in camera-type eye IEA
Inferred from Electronic Annotation
more info
  
involved_in symbiont entry into host cell NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in adherens junction IDA
Inferred from Direct Assay
more info
 PubMed 
located_in adherens junction NAS
Non-traceable Author Statement
more info
 PubMed 
located_in apical junction complex IEA
Inferred from Electronic Annotation
more info
  
located_in cell-cell contact zone IEA
Inferred from Electronic Annotation
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in growth cone membrane IEA
Inferred from Electronic Annotation
more info
  
located_in hippocampal mossy fiber to CA3 synapse IEA
Inferred from Electronic Annotation
more info
  
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in presynaptic active zone membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
nectin-1
Names
ectodermal dysplasia 4 (Margarita Island type)
herpes simplex virus type 1 sensitivity
herpes virus entry mediator C
herpesvirus Ig-like receptor
nectin 1
poliovirus receptor-like 1
poliovirus receptor-related 1 (herpesvirus entry mediator C)
poliovirus receptor-related protein 1

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_013083.2 RefSeqGene

    Range
    4526..72734
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002855.5 → NP_002846.3  nectin-1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002846.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1; also known as isoform Delta, alpha, or HveC).
    Source sequence(s)
    AI819997, AP003390, AP003393, BC021976, BC104948
    Consensus CDS
    CCDS8426.1
    UniProtKB/Swiss-Prot
    O75465, Q15223, Q2M3D3, Q9HBE6, Q9HBW2
    Related
    ENSP00000264025.3, ENST00000264025.8
    Conserved Domains (3) summary
    cd05886
    Location:45 → 143
    Ig1_Nectin-1_like; First immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
    cd05890
    Location:146 → 243
    Ig2_Nectin-1_like; Second immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
    cd00096
    Location:265 → 330
    Ig; Immunoglobulin domain

  2. NM_203285.2 → NP_976030.1  nectin-1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_976030.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses alternate exons for its 3' end, compared to variant 1, resulting in a protein (isoform 2; also known as isoform Alpha, beta, or HIgR) with a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AF110314, AI819997, AP003390
    UniProtKB/TrEMBL
    A0A8V8TKI1
    Related
    ENSP00000513010.1, ENST00000531468.2
    Conserved Domains (4) summary
    cd05886
    Location:45 → 143
    Ig1_Nectin-1_like; First immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
    cd05890
    Location:146 → 243
    Ig2_Nectin-1_like; Second immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
    smart00408
    Location:264 → 323
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:38 → 142
    IG_like; Immunoglobulin like

  3. NM_203286.2 → NP_976031.1  nectin-1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_976031.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate exon for its 3' end, compared to variant 1, resulting in a protein (isoform 3; also known as isoform Gamma) with a shorter and distinct C-terminus, compared to isoform 1. In contrast to isoforms 1 and 2, isoform 3 may be a soluble protein since it is predicted to lack a transmembrane domain.
    Source sequence(s)
    AI819997, AP003390, AY029539, BQ188335
    Consensus CDS
    CCDS8427.1
    UniProtKB/Swiss-Prot
    Q15223
    Related
    ENSP00000345289.2, ENST00000340882.2
    Conserved Domains (4) summary
    cd05886
    Location:45 → 143
    Ig1_Nectin-1_like; First immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
    cd05890
    Location:146 → 243
    Ig2_Nectin-1_like; Second immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
    smart00408
    Location:264 → 323
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:38 → 142
    IG_like; Immunoglobulin like

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    119638098..119729200 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    119660108..119752026 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_032767.1: Suppressed sequence

    Description
    NM_032767.1: This RefSeq was permanently suppressed because it was primarily UTR sequence.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15223.3 GenPept UniProtKB/Swiss-Prot:Q15223

Gene LinkOut

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