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

Summary

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

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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

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.
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.
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.
Loss of NECTIN1 triggers melanoma dissemination upon local IGF1 depletion.
Title: Loss of NECTIN1 triggers melanoma dissemination upon local IGF1 depletion.
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.
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.
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.
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.
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.
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 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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:483354

D11S3049 (e-PCR)
- UniSTS:152149

NoName (e-PCR)
- UniSTS:481412

SHGC-142781 (e-PCR)
- UniSTS:171655

SHGC-148300 (e-PCR)
- UniSTS:176307

D11S4421 (e-PCR)
- UniSTS:76488

A001W33 (e-PCR)
- UniSTS:17363

PVRL1__5616 (e-PCR)
- UniSTS:463837

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables cell adhesion mediator activity	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed

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 cochlea morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
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	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
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
is_active_in plasma membrane	IDA Inferred from Direct Assay 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

NG_013083.2 RefSeqGene

Range

4526..72734

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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