VCAM1 vascular cell adhesion molecule 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: VCAM1provided by HGNC
Official Full Name: vascular cell adhesion molecule 1provided by HGNC
Primary source: HGNC:HGNC:12663
See related: Ensembl:ENSG00000162692 MIM:192225; AllianceGenome:HGNC:12663
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: CD106; INCAM-100
Summary: This gene is a member of the Ig superfamily and encodes a cell surface sialoglycoprotein expressed by cytokine-activated endothelium. This type I membrane protein mediates leukocyte-endothelial cell adhesion and signal transduction, and may play a role in the development of artherosclerosis and rheumatoid arthritis. Three alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2010]
Expression: Biased expression in spleen (RPKM 208.8), lymph node (RPKM 52.3) and 7 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 1p21.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (100719742..100739045)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (100568139..100587438)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (101185298..101204601)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Analysis of ICAM-1 rs3093030, VCAM-1 rs3783605, and E-Selectin rs1805193 Polymorphisms in African Women Living with HIV and Preeclampsia.
Title: Analysis of ICAM-1 rs3093030, VCAM-1 rs3783605, and E-Selectin rs1805193 Polymorphisms in African Women Living with HIV and Preeclampsia.
TRIM65 Suppresses oxLDL-induced Endothelial Inflammation by Interaction with VCAM-1 in Atherogenesis.
Title: TRIM65 Suppresses oxLDL-induced Endothelial Inflammation by Interaction with VCAM-1 in Atherogenesis.
Differentiating Stages of Bipolar and Unipolar Depression-The Possible Role of sICAM-1 and sVCAM-1.
Title: Differentiating Stages of Bipolar and Unipolar Depression-The Possible Role of sICAM-1 and sVCAM-1.
Increased Expression of VCAM1 on Brain Endothelial Cells Drives Blood-Brain Barrier Impairment Following Chronic Cerebral Hypoperfusion.
Title: Increased Expression of VCAM1 on Brain Endothelial Cells Drives Blood-Brain Barrier Impairment Following Chronic Cerebral Hypoperfusion.
Interactions between integrin alpha9beta1 and VCAM-1 promote neutrophil hyperactivation and mediate poststroke DVT.
Title: Interactions between integrin α9β1 and VCAM-1 promote neutrophil hyperactivation and mediate poststroke DVT.
Endothelial cell-derived extracellular vesicles expressing surface VCAM1 promote sepsis-related acute lung injury by targeting and reprogramming monocytes.
Title: Endothelial cell-derived extracellular vesicles expressing surface VCAM1 promote sepsis-related acute lung injury by targeting and reprogramming monocytes.
Associations of Circulating Vascular Cell Adhesion Molecule-1 and Intercellular Adhesion Molecule-1 With Long-Term Cardiac Function.
Title: Associations of Circulating Vascular Cell Adhesion Molecule-1 and Intercellular Adhesion Molecule-1 With Long-Term Cardiac Function.
Elevated VCAM-1 levels in peripheral blood are associated with brain structural and functional alterations in major depressive disorder.
Title: Elevated VCAM-1 levels in peripheral blood are associated with brain structural and functional alterations in major depressive disorder.
Human IL-32theta;A94V mutant attenuates monocyte-endothelial adhesion by suppressing the expression of ICAM-1 and VCAM-1 via binding to cell surface receptor integrin alphaVbeta3 and alphaVbeta6 in TNF-alpha-stimulated HUVECs.
Title: Human IL-32θA94V mutant attenuates monocyte-endothelial adhesion by suppressing the expression of ICAM-1 and VCAM-1 via binding to cell surface receptor integrin αVβ3 and αVβ6 in TNF-α-stimulated HUVECs.
EPSTI1 promotes monocyte adhesion to endothelial cells in vitro via upregulating VCAM-1 and ICAM-1 expression.
Title: EPSTI1 promotes monocyte adhesion to endothelial cells in vitro via upregulating VCAM-1 and ICAM-1 expression.

Submit: New GeneRIF Correction See all GeneRIFs (488)

Phenotypes

Go to the top of the page Help

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
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

Replication interactions

Interaction	Pubs
HIV-1/HCV co-infection correlates with elevated ICAM1 and VCAM1 serum levels, which relates to disease progression	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 activates human brain micro vascular endothelial cells (HBMEC) via CD4 in upregulating ICAM-1 and VCAM-1 expression, IL-6 secretion and increased monocyte transmigration across monolayers	PubMed
Tat	tat	HIV-1 Tat upregulates VCAM1 protein expression in hCMEC/D3 cells	PubMed
	tat	HIV-1 Tat upregulates VCAM1 mRNA and protein expression in CRT-MG human astroglioma cells	PubMed
	tat	HIV-1 Tat upregulates the expression of VCAM-1 in endothelial cells and astrocytes, an effect that is in part regulated by NF-kappa B and may be associated with AIDS-related Kaposi's sarcoma	PubMed
	tat	Cell-permeable SOD inhibits the activation of MAP kinases including ERK, JNK and p38 and the upregulation of ICAM-1 and VCAM-1 by HIV-1 Tat	PubMed
	tat	HIV-1 Tat-induced upregulation of VCAM-1/ICAM-1 is blocked by NADPH oxidase inhibitor	PubMed
Vpu	vpu	HIV-1 Vpu upregulates CD40 expression, which enhances efficient expression of VCAM-1 in endothelial cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

SGV-R136 (e-PCR)
- UniSTS:254208

SGV-R137 (e-PCR)
- UniSTS:254209

SGV-R144 (e-PCR)
- UniSTS:254210

SGV-R165 (e-PCR)
- UniSTS:254211

SGV-R169 (e-PCR)
- UniSTS:254212

SGV-R170 (e-PCR)
- UniSTS:254213

SGV-R171 (e-PCR)
- UniSTS:254214

SGV-R173 (e-PCR)
- UniSTS:254216

SGV-R178 (e-PCR)
- UniSTS:254217

SGV-R230 (e-PCR)
- UniSTS:254218

SGV-R231 (e-PCR)
- UniSTS:254219

SGV-R232 (e-PCR)
- UniSTS:254220

SGV-R233 (e-PCR)
- UniSTS:254221

SGV-R234 (e-PCR)
- UniSTS:254222

SGV-R235 (e-PCR)
- UniSTS:254223

SGV-R236 (e-PCR)
- UniSTS:254224

SGV-R239 (e-PCR)
- UniSTS:254225

SGV-R240 (e-PCR)
- UniSTS:254226

GDB:216806 (e-PCR)
- UniSTS:156215

GDB:192501 (e-PCR)
- UniSTS:155724

VCAM1_385 (e-PCR)
- UniSTS:277859

SHGC-12401 (e-PCR)
- UniSTS:38003

AL009440 (e-PCR)
- UniSTS:121

AL010034 (e-PCR)
- UniSTS:52859

WI-18941 (e-PCR)
- UniSTS:80002

RH39988 (e-PCR)
- UniSTS:86683

AL034328 (e-PCR)
- UniSTS:94154

SGV-R135 (e-PCR)
- UniSTS:254207

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cell adhesion mediator activity	IDA Inferred from Direct Assay more info	PubMed
enables cell adhesion molecule binding	IDA Inferred from Direct Assay more info	PubMed
enables cell adhesion molecule binding	IPI Inferred from Physical Interaction more info	PubMed
enables integrin binding	IBA Inferred from Biological aspect of Ancestor more info
enables integrin binding	IDA Inferred from Direct Assay more info	PubMed
enables integrin binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables primary methylamine oxidase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in B cell differentiation	IC Inferred by Curator more info	PubMed
involved_in amine metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in cardiac neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in cell chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in cell-cell adhesion mediated by integrin	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cell-matrix adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to amyloid-beta	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to tumor necrosis factor	IEA Inferred from Electronic Annotation more info
involved_in cellular response to vascular endothelial growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in chronic inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	IDA Inferred from Direct Assay more info	PubMed
involved_in heterotypic cell-cell adhesion	IGI Inferred from Genetic Interaction more info	PubMed
involved_in inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in innervation	IEA Inferred from Electronic Annotation more info
involved_in leukocyte cell-cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in leukocyte tethering or rolling	IDA Inferred from Direct Assay more info	PubMed
involved_in leukocyte tethering or rolling	IEP Inferred from Expression Pattern more info	PubMed
involved_in membrane to membrane docking	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of T cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in response to ethanol	IEA Inferred from Electronic Annotation more info
involved_in response to hypoxia	IEA Inferred from Electronic Annotation more info
involved_in response to ionizing radiation	IEA Inferred from Electronic Annotation more info
involved_in response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in response to nicotine	IEA Inferred from Electronic Annotation more info
involved_in response to nutrient	IEA Inferred from Electronic Annotation more info
involved_in response to zinc ion	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
part_of alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex	IDA Inferred from Direct Assay more info	PubMed
located_in apical part of cell	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in external side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in filopodium	IDA Inferred from Direct Assay more info	PubMed
located_in microvillus	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IC Inferred by Curator more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in podosome	IDA Inferred from Direct Assay more info	PubMed
located_in sarcolemma	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: vascular cell adhesion protein 1

Names: CD106 antigen

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_023034.2 RefSeqGene

Range

5002..24305

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001078.4 → NP_001069.1 vascular cell adhesion protein 1 isoform a precursor

See identical proteins and their annotated locations for NP_001069.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the predominant, full-length isoform (a).

Source sequence(s)

BC017276, BF791565, DB096825

Consensus CDS

CCDS773.1

UniProtKB/Swiss-Prot

A8K6R7, B4DKS4, E9PDD1, P19320, Q6NUP8

UniProtKB/TrEMBL

Q53FL7

Related

ENSP00000294728.2, ENST00000294728.7

Conserved Domains (5) summary

cd07689
Location:116 → 214

Ig_VCAM-1; Immunoglobulin (Ig)-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1, CD106) and intercellular cell adhesion molecule-1 (ICAM-1, CD54) and similar domains

smart00408
Location:238 → 298

IGc2; Immunoglobulin C-2 Type

smart00409
Location:33 → 112

IG; Immunoglobulin

smart00410
Location:519 → 596

IG_like; Immunoglobulin like

cl28434
Location:313 → 399

I-set; Immunoglobulin I-set domain
NM_001199834.2 → NP_001186763.1 vascular cell adhesion protein 1 isoform c precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame segment in the CDS compared to transcript variant 1. The resulting isoform (c) lacks an internal segment compared to isoform a.

Source sequence(s)

AK296692, BC017276, BF968655

Consensus CDS

CCDS55617.1

UniProtKB/TrEMBL

Q53FL7

Related

ENSP00000359137.3, ENST00000370119.8

Conserved Domains (4) summary

cd07689
Location:54 → 152

Ig2_VCAM-1; Second immunoglobulin (Ig)-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1, CD106) and intercellular cell adhesion molecule-1 (ICAM-1, CD54) and similar proteins

smart00408
Location:176 → 236

IGc2; Immunoglobulin C-2 Type

smart00410
Location:259 → 337

IG_like; Immunoglobulin like

pfam13927
Location:546 → 610

Ig_3; Immunoglobulin domain
NM_080682.3 → NP_542413.1 vascular cell adhesion protein 1 isoform b precursor

See identical proteins and their annotated locations for NP_542413.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the CDS compared to transcript variant 1. The resulting isoform (b) lacks an internal segment compared to isoform a.

Source sequence(s)

BC017276, BF791565, DB096825, M30257

Consensus CDS

CCDS774.1

UniProtKB/TrEMBL

Q53FL7

Related

ENSP00000304611.2, ENST00000347652.6

Conserved Domains (5) summary

cd07689
Location:116 → 214

Ig2_VCAM-1; Second immunoglobulin (Ig)-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1, CD106) and intercellular cell adhesion molecule-1 (ICAM-1, CD54) and similar proteins

smart00408
Location:238 → 298

IGc2; Immunoglobulin C-2 Type

smart00410
Location:33 → 112

IG_like; Immunoglobulin like

pfam00047
Location:35 → 97

ig; Immunoglobulin domain

pfam13927
Location:516 → 580

Ig_3; Immunoglobulin domain