ITGA10
protein-codingintegrin subunit alpha 10, the group of Integrin alpha subunits
Gene summary
Integrins are integral transmembrane glycoproteins composed of noncovalently linked alpha and beta chains. They participate in cell adhesion as well as cell-surface mediated signalling. This gene encodes an integrin alpha chain and is expressed at high levels in chondrocytes, where it is transcriptionally regulated by AP-2epsilon and Ets-1. The protein encoded by this gene binds to collagen. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ITGA10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003637.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 161 | 3 | 164 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 162 | 4 | 0 | 166 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003628.2 | 30 | MANE Select | |
| Ensembl | ENSP00000358310.3 | 30 | MANE Select | |
| RefSeq | NP_001289969.1 | 26 | Standard | |
| RefSeq | NP_001289970.1 | 26 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| itga10 | Danio rerio | Structure: skeletal tissue Quality: decreased area abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- PI3K-Akt signaling pathway - 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)
Biological Process
- cell-matrix adhesion
- integrin-mediated signaling pathway
- extracellular matrix organization
Molecular Function
- collagen binding
- metal ion binding
- collagen binding involved in cell-matrix adhesion
Cellular Component
- plasma membrane
- integrin complex
- integrin alpha10-beta1 complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369304
- Coding exons
- 30
- Length
- 18978
- Individuals with no LoFs
- 125548
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 200
- Defined
- 125748
- p
- 0.000796
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.881 | 587 | 650 | 0.903 | 0.0000355 | 7475 |
| Missense (PolyPhen) | 210 | 232.07 | 0.90489 | 2764 | ||
| Synonymous | 0.862 | 232 | 249 | 0.931 | 0.0000121 | 2475 |
| Loss of Function | 3.01 | 41 | 67.8 | 0.605 | 0.00000410 | 682 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00074 | 0.00074 | rare |
| Latino/Admixed American | 0.0013 | 0.0013 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00098 | 0.00098 | rare |
| Finnish | 0.00046 | 0.00046 | rare |
| European (Non-Finnish) | 0.00079 | 0.00078 | rare |
| South Asian | 0.00072 | 0.00069 | rare |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Integrin alpha-10/beta-1 is a receptor for collagen.;
Recessive Scores
- pRec
- 0.165
Intolerance Scores
- LoFtool
- 0.788
- RVIS EVS
- 1.27
- RVIS percentile EVS
- 93.67
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.651
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |