ITGAD
protein-codingintegrin subunit alpha D, the group of Integrin alpha subunits|CD molecules
Gene summary
This gene belongs to the beta-2 integrin family of membrane glycoproteins, which are are composed of non-covalently linked alpha and beta subunits to form a heterodimer. It encodes the alpha subunit of the cell surface heterodimers and is involved in the activation and adhesion functions of leukocytes. The gene is located about 11kb downstream of the integrin subunit alpha X gene, another member of the integrin family. It is expressed in the tissue and circulating myeloid leukocytes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.2 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 ITGAD variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005353.3. 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 | 176 | 11 | 187 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 178 | 12 | 0 | 190 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005344.2 | 30 | MANE Select | |
| Ensembl | ENSP00000373854.2 | 30 | MANE Select | |
| RefSeq | NP_001305114.1 | 30 | Standard | |
| Ensembl | ENSP00000800956.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Regulation of actin cytoskeleton - Homo sapiens (human)
- Integrin-mediated Cell Adhesion
- Focal Adhesion
- Overview of nanoparticle effects
- Focal Adhesion-PI3K-Akt-mTOR-signaling pathway
Biological Process
- immune response
- integrin-mediated signaling pathway
- extracellular matrix organization
- heterotypic cell-cell adhesion
Molecular Function
- metal ion binding
Cellular Component
- plasma membrane
- integrin complex
- cell surface
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000389202
- Coding exons
- 30
- Length
- 33194
- Individuals with no LoFs
- 125113
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 634
- Defined
- 125748
- p
- 0.00253
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.850 | 628 | 691 | 0.909 | 0.0000404 | 7560 |
| Missense (PolyPhen) | 180 | 201.27 | 0.89433 | 2241 | ||
| Synonymous | -1.02 | 315 | 293 | 1.08 | 0.0000190 | 2343 |
| Loss of Function | 2.44 | 43 | 64.0 | 0.672 | 0.00000330 | 676 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0033 | 0.0033 | notable |
| Latino/Admixed American | 0.0019 | 0.0018 | notable |
| Ashkenazi Jewish | 0.00089 | 0.00089 | rare |
| East Asian | 0.0023 | 0.0023 | notable |
| Finnish | 0.0015 | 0.0014 | notable |
| European (Non-Finnish) | 0.0032 | 0.0031 | notable |
| South Asian | 0.0022 | 0.0022 | notable |
| Other | 0.0030 | 0.0029 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Integrin alpha-D/beta-2 is a receptor for ICAM3 and VCAM1. May play a role in the atherosclerotic process such as clearing lipoproteins from plaques and in phagocytosis of blood- borne pathogens, particulate matter, and senescent erythrocytes from the blood.;
Intolerance Scores
- LoFtool
- 0.604
- RVIS EVS
- -0.52
- RVIS percentile EVS
- 20.97
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.781
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |