ITGA9
integrin subunit alpha 9, the group of Integrin alpha subunits
Basic information
Region (hg38): 3:37452115-37823507
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (121 variants)
- ITGA9-related_disorder (23 variants)
- not_provided (13 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. These statistics are base on transcript: NM_000002207.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 16 | |||||
| missense | 119 | 129 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 119 | 15 | 11 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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