NECTIN3 nectin cell adhesion molecule 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NECTIN3provided by HGNC
Official Full Name: nectin cell adhesion molecule 3provided by HGNC
Primary source: HGNC:HGNC:17664
See related: Ensembl:ENSG00000177707 MIM:607147; AllianceGenome:HGNC:17664
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: PPR3; PRR3; CD113; PVRL3; PVRR3; CDW113; NECTIN-3
Summary: This gene encodes a member of the nectin family of proteins, which function as adhesion molecules at adherens junctions. This family member interacts with other nectin-like proteins and with afadin, a filamentous actin-binding protein involved in the regulation of directional motility, cell proliferation and survival. This gene plays a role in ocular development involving the ciliary body. Mutations in this gene are believed to result in congenital ocular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Expression: Broad expression in thyroid (RPKM 7.4), testis (RPKM 7.4) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q13.13

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (111071816..111194170)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (113792242..113914605)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (110790663..110913017)

Chromosome 3 - NC_000003.12 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 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?

Loss of nectin-3 expression as a marker of tumor aggressiveness in pancreatic neuroendocrine tumor.
Title: Loss of nectin-3 expression as a marker of tumor aggressiveness in pancreatic neuroendocrine tumor.
Nectin-3 expression was associated with ovarian cancer, and a greater expression level of nectin-3 was related to poor overall survival.
Title: Nectin-3 is a new biomarker that mediates the upregulation of MMP2 and MMP9 in ovarian cancer cells.
Nectin-3 mutation in men with severe teratospermia
Title: Detection of candidate nectin gene mutations in infertile men with severe teratospermia.
Data suggest that 3 independent regions of TcdB (Clostridium difficile toxin B; 1372-1493, 1493-1848, 1851-2366) contribute to binding and entry of TcdB into mammalian cells; residues 1372-1493 are sufficient for interaction with PVRL3.
Title: Binding and entry of Clostridium difficile toxin B is mediated by multiple domains.
Expression of nectin-3 in pancreatic cancer can be a prognostic factor.
Title: Nectin expression in pancreatic adenocarcinoma: nectin-3 is associated with a poor prognosis.
PVRL3 is a physiologically relevant binding partner that can serve as a target for the prevention of TcdB-induced cytotoxicity in C. difficile infection.
Title: Identification of an epithelial cell receptor responsible for Clostridium difficile TcdB-induced cytotoxicity.
Nectin-3 is associated with the formation of cell junctions and be a putative suppressor molecule to the invasion of breast cancer cells.
Title: The expression of the Nectin complex in human breast cancer and the role of Nectin-3 in the control of tight junctions during metastasis.
Nectin-3 trans-interacts with Nectin-2 to promote lymphocyte and monocyte extravasation.
Title: Nectin-3 (CD113) interacts with Nectin-2 (CD112) to promote lymphocyte transendothelial migration.
Data suggest that expression of nectin-3 is up-regulated in eutopic endometrium of patients with endometriosis as compared with control subjects and up-regulated in all endometriotic lesions investigated compared with eutopic endometrium.
Title: Eutopic endometrium and peritoneal, ovarian and colorectal endometriotic tissues express a different profile of nectin-1, -3, -4 and nectin-like molecule 2.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.

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

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 NECTIN3	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat downregulates the expression of poliovirus receptor-related 3 (PVRL3) in human primary T cells	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

D3S3921 (e-PCR)
- UniSTS:793

STS-R78584 (e-PCR)
- UniSTS:48187

RH93019 (e-PCR)
- UniSTS:84587

RH94030 (e-PCR)
- UniSTS:91797

RH125725 (e-PCR)
- UniSTS:162484

RH47398 (e-PCR)
- UniSTS:1470

PVRL3__5617 (e-PCR)
- UniSTS:463838

SHGC-77178 (e-PCR)
- UniSTS:41701

RH12011 (e-PCR)
- UniSTS:74221

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	IPI Inferred from Physical Interaction 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

Process	Evidence Code	Pubs
involved_in establishment of protein localization to plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in fertilization	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 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 lens morphogenesis in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in protein localization to cell junction	IEA Inferred from Electronic Annotation more info
involved_in regulation of postsynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in retina morphogenesis in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in symbiont entry into host cell	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
is_active_in apical junction complex	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cell-cell contact zone	IEA Inferred from Electronic Annotation more info
located_in cell-cell junction	ISS Inferred from Sequence or Structural Similarity more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in hippocampal mossy fiber to CA3 synapse	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: nectin-3

Names: nectin 3; poliovirus receptor-related 3; poliovirus receptor-related protein 3

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_029835.1 RefSeqGene

Range

5058..70802

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001243286.2 → NP_001230215.1 nectin-3 isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.

Source sequence(s)

AA555086, AC133477, AC137833, BC067808, BI464010

Consensus CDS

CCDS58842.1

UniProtKB/Swiss-Prot

Q9NQS3

Related

ENSP00000321514.3, ENST00000319792.7

Conserved Domains (4) summary

cd00096
Location:269 → 275

Ig; Ig strand A [structural motif]

cd05887
Location:58 → 167

IgV_1_Nectin-3_like; First immunoglobulin variable (IgV) domain of nectin-3 (also known as poliovirus receptor related protein 3), and similar domains

cd07704
Location:170 → 265

IgC1_2_Nectin-3-4_like; Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related protein 4), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains

cl11960
Location:269 → 355

Ig; Immunoglobulin domain
NM_001243288.2 → NP_001230217.1 nectin-3 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region, uses a distinct start codon, and has alternate exon structure in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has distinct N- and C-termini and is shorter than isoform 1.

Source sequence(s)

AC133436, AC133477, AK075105, BQ025085

Consensus CDS

CCDS58843.1

UniProtKB/Swiss-Prot

Q9NQS3

Related

ENSP00000420579.1, ENST00000493615.5

Conserved Domains (4) summary

cd05887
Location:49 → 144

Ig1_Nectin-3_like; First immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3) and similar proteins

smart00410
Location:41 → 143

IG_like; Immunoglobulin like

pfam13927
Location:264 → 319

Ig_3; Immunoglobulin domain

cl11960
Location:147 → 242

Ig; Immunoglobulin domain
NM_015480.3 → NP_056295.1 nectin-3 isoform 1 precursor

See identical proteins and their annotated locations for NP_056295.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AA555086, AC137833, AF282874, BI464010

Consensus CDS

CCDS2957.1

UniProtKB/Swiss-Prot

E9PFR0, Q6NVZ3, Q8NC05, Q8WVU4, Q9BVA9, Q9NQS3, Q9Y412

Related

ENSP00000418070.1, ENST00000485303.6

Conserved Domains (5) summary

cd12087
Location:404 → 432

TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases

cd00096
Location:269 → 275

Ig; Ig strand A [structural motif]

cd05887
Location:58 → 167

IgV_1_Nectin-3_like; First immunoglobulin variable (IgV) domain of nectin-3 (also known as poliovirus receptor related protein 3), and similar domains

cd07704
Location:170 → 265

IgC1_2_Nectin-3-4_like; Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related protein 4), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains

cl11960
Location:269 → 355

Ig; Immunoglobulin domain

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_000003.12 Reference GRCh38.p14 Primary Assembly

Range

111071816..111194170

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017006123.2 → XP_016861612.1 nectin-3 isoform X2
XM_017006126.2 → XP_016861615.1 nectin-3 isoform X5
XM_017006125.2 → XP_016861614.1 nectin-3 isoform X4
XM_011512663.2 → XP_011510965.1 nectin-3 isoform X1

Conserved Domains (5) summary

cd05887
Location:103 → 198

Ig1_Nectin-3_like; First immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3) and similar proteins

cd12087
Location:435 → 463

TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases

smart00410
Location:95 → 197

IG_like; Immunoglobulin like

pfam13927
Location:318 → 373

Ig_3; Immunoglobulin domain

cl11960
Location:201 → 296

Ig; Immunoglobulin domain
XM_047447934.1 → XP_047303890.1 nectin-3 isoform X6
XM_017006127.3 → XP_016861616.1 nectin-3 isoform X6

Conserved Domains (4) summary

cd12087
Location:192 → 220

TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases

smart00410
Location:75 → 136

IG_like; Immunoglobulin like

pfam13927
Location:75 → 130

Ig_3; Immunoglobulin domain

cl11960
Location:1 → 53

Ig; Immunoglobulin domain
XM_017006124.2 → XP_016861613.1 nectin-3 isoform X3