ITGA9

integrin subunit alpha 9, the group of Integrin alpha subunits

Basic information

Region (hg38): 3:37452114-37823507

Links

ENSG00000144668 ∙ NCBI:3680 ∙ OMIM:603963 ∙ HGNC:6145 ∙ Uniprot:Q13797 ∙ 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 ITGA9 gene.

• Inborn genetic diseases (40 variants)
• not provided (11 variants)
• not specified (6 variants)
• ITGA9-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGA9 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				2	6	8
missense			39	2	5	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					3	3
Total	0	0	39	4	14

Variants in ITGA9

This is a list of pathogenic ClinVar variants found in the ITGA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-37452394-C-G		not specified	Uncertain significance (Nov 03, 2022)
3-37452400-G-A		not specified	Uncertain significance (Jul 12, 2022)
3-37452408-A-C			Likely benign (Jan 19, 2018)
3-37452439-T-G		not specified	Uncertain significance (Nov 16, 2021)
3-37471048-C-G		not specified	Uncertain significance (Dec 18, 2023)
3-37471115-C-A		ITGA9-related disorder	Benign (Feb 18, 2020)
3-37473363-G-T		not specified	Uncertain significance (Aug 26, 2022)
3-37473369-C-T		ITGA9-related disorder	Likely benign (Feb 11, 2022)
3-37473453-G-A		not specified	Uncertain significance (Feb 21, 2024)
3-37481496-C-T		not specified	Uncertain significance (Apr 25, 2023)
3-37481497-G-A		not specified	Uncertain significance (Jan 04, 2024)
3-37481522-C-T			Likely benign (Nov 01, 2023)
3-37481523-G-A		not specified	Uncertain significance (Feb 26, 2024)
3-37481544-T-C		not specified	Uncertain significance (Aug 02, 2023)
3-37494493-C-G		not specified • ITGA9-related disorder	Benign (Aug 02, 2019)
3-37494565-C-T		not specified	Benign (Mar 28, 2016)
3-37503245-C-A		not specified	Uncertain significance (Dec 08, 2023)
3-37503251-A-G		not specified	Uncertain significance (Dec 20, 2023)
3-37506010-G-A			Benign (Jun 08, 2018)
3-37506014-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-37506062-C-T		not specified	Uncertain significance (Nov 03, 2022)
3-37508581-G-A		not specified	Uncertain significance (Jul 19, 2023)
3-37508677-T-A		not specified	Benign (Feb 09, 2017)
3-37513782-C-T		not specified	Uncertain significance (Sep 22, 2023)
3-37513792-C-G		not specified	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGA9	protein_coding	protein_coding	ENST00000264741	28	371400

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00816	0.992	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.627	532	574	0.926	0.0000349	6774
Missense in Polyphen		182	224.06	0.8123		2640
Synonymous	-1.00	245	226	1.08	0.0000153	2012
Loss of Function	4.99	15	54.9	0.273	0.00000280	650

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000984	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin alpha-9/beta-1 (ITGA9:ITGB1) is a receptor for VCAM1, cytotactin and osteopontin. It recognizes the sequence A-E- I-D-G-I-E-L in cytotactin. {ECO:0000250}.
• 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);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;Developmental Biology;Integrin cell surface interactions;Extracellular matrix organization;Integrin;Signal transduction by L1;Arf6 trafficking events;L1CAM interactions;Plexin-D1 Signaling;Axon guidance;ECM proteoglycans;Alpha9 beta1 integrin signaling events;Beta1 integrin cell surface interactions (Consensus)

Recessive Scores

• pRec: 0.283

Intolerance Scores

• loftool: 0.555
• rvis_EVS: -1.1
• rvis_percentile_EVS: 6.95

Haploinsufficiency Scores

• pHI: 0.157
• hipred: Y
• hipred_score: 0.668
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.751

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itga9
• Phenotype: immune system phenotype; vision/eye phenotype; normal 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); 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); respiratory system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: itga9
• Affected structure: lymphangioblast cord
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cell adhesion;integrin-mediated signaling pathway;extracellular matrix organization;neutrophil chemotaxis;wound healing
• Cellular component: plasma membrane;integrin complex;basal plasma membrane;integrin alpha9-beta1 complex
• Molecular function: collagen binding;laminin binding;metal ion binding