VCAM1

vascular cell adhesion molecule 1, the group of CD molecules|C2-set domain containing|Ig-like cell adhesion molecule family|I-set domain containing|Receptor ligands

Basic information

Region (hg38): 1:100719741-100739045

Links

ENSG00000162692 ∙ NCBI:7412 ∙ OMIM:192225 ∙ HGNC:12663 ∙ Uniprot:P19320 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VCAM1 gene.

• Inborn genetic diseases (24 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VCAM1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			22	2	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	22	7	1

Variants in VCAM1

This is a list of pathogenic ClinVar variants found in the VCAM1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-100719885-C-T		not specified	Likely benign (Feb 10, 2023)
1-100719891-G-A		not specified	Uncertain significance (May 16, 2022)
1-100719897-A-T		not specified	Uncertain significance (Jun 18, 2021)
1-100720518-T-G		not specified	Uncertain significance (Mar 13, 2023)
1-100720528-T-C			Likely benign (Aug 15, 2018)
1-100720626-C-T		not specified	Uncertain significance (Sep 15, 2021)
1-100720647-C-T		not specified	Uncertain significance (Mar 05, 2024)
1-100720649-C-G		not specified	Uncertain significance (Sep 17, 2021)
1-100723011-C-T			Likely benign (Mar 29, 2018)
1-100723065-C-T		not specified	Likely benign (Oct 26, 2021)
1-100723148-C-A		not specified	Uncertain significance (Feb 17, 2022)
1-100723181-G-A		not specified	Uncertain significance (Jun 10, 2022)
1-100723190-A-G		not specified	Uncertain significance (Jul 16, 2021)
1-100723256-C-A		not specified	Uncertain significance (Mar 01, 2023)
1-100723293-A-G		not specified	Uncertain significance (Jun 30, 2023)
1-100724703-C-T			Likely benign (May 09, 2018)
1-100724706-C-T			Likely benign (Jun 01, 2022)
1-100724743-A-C		not specified	Uncertain significance (Sep 12, 2023)
1-100724759-A-C		not specified	Uncertain significance (Aug 12, 2021)
1-100724861-A-G		not specified	Uncertain significance (Mar 28, 2023)
1-100724864-G-A		not specified	Uncertain significance (Jan 02, 2024)
1-100729127-A-G		not specified	Uncertain significance (May 23, 2023)
1-100729188-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-100729190-A-G		not specified	Uncertain significance (Dec 06, 2022)
1-100729373-G-C		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VCAM1	protein_coding	protein_coding	ENST00000294728	9	19304

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.798	0.202	125713	0	19	125732	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	322	389	0.828	0.0000191	4838
Missense in Polyphen		84	129.99	0.64622		1725
Synonymous	0.732	139	150	0.924	0.00000837	1444
Loss of Function	3.95	5	27.3	0.183	0.00000131	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000236	0.000236
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important in cell-cell recognition. Appears to function in leukocyte-endothelial cell adhesion. Interacts with integrin alpha-4/beta-1 (ITGA4/ITGB1) on leukocytes, and mediates both adhesion and signal transduction. The VCAM1/ITGA4/ITGB1 interaction may play a pathophysiologic role both in immune responses and in leukocyte emigration to sites of inflammation.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);African trypanosomiasis - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Malaria - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase;RANKL-RANK (Receptor activator of NFKB (ligand)) Signaling Pathway;Photodynamic therapy-induced NF-kB survival signaling;Amplification and Expansion of Oncogenic Pathways as Metastatic Traits;Interleukin-4 and 13 signaling;Cytokine Signaling in Immune system;Integrin cell surface interactions;Extracellular matrix organization;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Thromboxane A2 receptor signaling;Interferon gamma signaling;a4b7 Integrin signaling;Alpha9 beta1 integrin signaling events;Interferon Signaling;Beta5 beta6 beta7 and beta8 integrin cell surface interactions;Beta1 integrin cell surface interactions;Alpha4 beta1 integrin signaling events;Cellular roles of Anthrax toxin;Beta2 integrin cell surface interactions (Consensus)

Recessive Scores

• pRec: 0.748

Intolerance Scores

• loftool: 0.518
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.416
• hipred: Y
• hipred_score: 0.667
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.593

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vcam1
• Phenotype: immune system phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: response to hypoxia;acute inflammatory response;chronic inflammatory response;cell adhesion;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;leukocyte cell-cell adhesion;cell-matrix adhesion;aging;response to nutrient;amine metabolic process;response to zinc ion;response to ionizing radiation;cytokine-mediated signaling pathway;membrane to membrane docking;B cell differentiation;extracellular matrix organization;response to lipopolysaccharide;response to nicotine;calcium-mediated signaling using intracellular calcium source;cellular response to vascular endothelial growth factor stimulus;positive regulation of T cell proliferation;response to ethanol;regulation of immune response;leukocyte tethering or rolling;oxidation-reduction process;cell chemotaxis;interferon-gamma-mediated signaling pathway;innervation;cardiac neuron differentiation;cellular response to tumor necrosis factor
• Cellular component: podosome;extracellular space;early endosome;endoplasmic reticulum;Golgi apparatus;plasma membrane;integral component of plasma membrane;microvillus;external side of plasma membrane;cell surface;filopodium;sarcolemma;apical part of cell;extracellular exosome;alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex
• Molecular function: integrin binding;primary amine oxidase activity;cell adhesion molecule binding