ITGB7

integrin subunit beta 7, the group of Integrin beta subunits

Basic information

Region (hg38): 12:53191322-53207282

Links

ENSG00000139626 ∙ NCBI:3695 ∙ OMIM:147559 ∙ HGNC:6162 ∙ Uniprot:P26010 ∙ 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 ITGB7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGB7 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			30	4	2	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	4	6

Variants in ITGB7

This is a list of pathogenic ClinVar variants found in the ITGB7 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53191634-G-C		not specified	Uncertain significance (May 06, 2022)
12-53191865-C-A		not specified	Uncertain significance (Aug 22, 2023)
12-53191891-C-G		not specified	Uncertain significance (Apr 01, 2024)
12-53191897-G-A		not specified	Uncertain significance (Jan 29, 2024)
12-53191909-G-A		not specified	Uncertain significance (May 13, 2024)
12-53191929-G-A		not specified	Uncertain significance (Oct 02, 2023)
12-53191935-C-T		not specified	Uncertain significance (Oct 27, 2022)
12-53191947-A-G		not specified	Uncertain significance (Mar 01, 2023)
12-53192004-G-A		not specified	Uncertain significance (Jun 10, 2024)
12-53192341-C-T		not specified	Uncertain significance (Jun 17, 2024)
12-53192459-T-G		not specified	Uncertain significance (Mar 27, 2023)
12-53192471-G-A			Benign (May 21, 2018)
12-53192479-G-C		not specified	Uncertain significance (Nov 18, 2022)
12-53192490-G-A			Benign (Dec 31, 2019)
12-53192701-C-T		not specified	Uncertain significance (Oct 12, 2022)
12-53192735-T-C			Benign (Dec 31, 2019)
12-53192752-C-T			Benign (Mar 29, 2018)
12-53192784-C-T		not specified	Likely benign (Jan 16, 2024)
12-53192893-A-G		not specified	Uncertain significance (Dec 20, 2021)
12-53192902-G-A		not specified	Uncertain significance (Jun 11, 2024)
12-53193163-C-T		not specified	Uncertain significance (Oct 13, 2023)
12-53193226-C-T		not specified	Likely benign (Jan 23, 2023)
12-53193262-G-A		not specified	Uncertain significance (Dec 11, 2023)
12-53193283-C-T		not specified	Uncertain significance (Dec 03, 2021)
12-53193340-C-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGB7	protein_coding	protein_coding	ENST00000267082	14	15990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000237	1.00	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	394	482	0.818	0.0000292	5150
Missense in Polyphen		136	192.3	0.70723		2100
Synonymous	-1.30	219	196	1.12	0.0000117	1632
Loss of Function	3.25	16	37.5	0.427	0.00000185	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000109	0.000109
South Asian	0.0000985	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin alpha-4/beta-7 (Peyer patches-specific homing receptor LPAM-1) is an adhesion molecule that mediates lymphocyte migration and homing to gut-associated lymphoid tissue (GALT). Integrin alpha-4/beta-7 interacts with the cell surface adhesion molecules MADCAM1 which is normally expressed by the vascular endothelium of the gastrointestinal tract. Interacts also with VCAM1 and fibronectin, an extracellular matrix component. It recognizes one or more domains within the alternatively spliced CS-1 region of fibronectin. Interactions involves the tripeptide L-D-T in MADCAM1, and L-D-V in fibronectin. Binds to HIV-1 gp120, thereby allowing the virus to enter GALT, which is thought to be the major trigger of AIDS disease. Interaction would involve a tripeptide L-D-I in HIV-1 gp120. Integrin alpha-E/beta-7 (HML-1) is a receptor for E-cadherin.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Cell adhesion molecules (CAMs) - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Dilated cardiomyopathy (DCM) - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Integrin-mediated Cell Adhesion;Arrhythmogenic Right Ventricular Cardiomyopathy;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Integrin cell surface interactions;Extracellular matrix organization;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Integrin;AlphaE beta7 integrin cell surface interactions;a4b7 Integrin signaling;Beta5 beta6 beta7 and beta8 integrin cell surface interactions;E-cadherin signaling in the nascent adherens junction (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• loftool: 0.143
• rvis_EVS: -1.35
• rvis_percentile_EVS: 4.63

Haploinsufficiency Scores

• pHI: 0.110
• hipred: Y
• hipred_score: 0.595
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itgb7
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; embryo phenotype; immune system phenotype; skeleton phenotype; digestive/alimentary phenotype; reproductive system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cell-matrix adhesion involved in ameboidal cell migration;cell adhesion;cell-matrix adhesion;integrin-mediated signaling pathway;cell migration;extracellular matrix organization;cell adhesion mediated by integrin;heterotypic cell-cell adhesion;substrate adhesion-dependent cell spreading;receptor clustering;viral entry into host cell;regulation of immune response;leukocyte tethering or rolling;T cell migration
• Cellular component: plasma membrane;focal adhesion;integrin complex;cell surface;membrane;integrin alpha4-beta7 complex;receptor complex;extracellular exosome
• Molecular function: virus receptor activity;integrin binding;protein binding;signaling receptor activity;metal ion binding;cell adhesion molecule binding