CORO1A
coronin 1A, the group of WD repeat domain containing|Coronins
Basic information
Region (hg38): 16:30182827-30189076
Links
Phenotypes
GenCC
Source:
- epidermodysplasia verruciformis (Moderate), mode of inheritance: AR
- severe combined immunodeficiency due to CORO1A deficiency (Moderate), mode of inheritance: AR
- severe combined immunodeficiency due to CORO1A deficiency (Strong), mode of inheritance: AR
- severe combined immunodeficiency due to CORO1A deficiency (Supportive), mode of inheritance: AR
- autism spectrum disorder (Limited), mode of inheritance: AD
- severe combined immunodeficiency due to CORO1A deficiency (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Immunodeficiency 8 with lymphoproliferation | AR | Allergy/Immunology/Infectious; Oncologic | The condition can involve recurrent infections, and awareness may allow preventive measures, and early and aggressive treatment of infections; Individuals have been described with oncologic sequelae of infections (such as EBV-related lymphoproliferative disorders) and awareness may allow prompt diagnosis and management; BMT has been described | Allergy/Immunology/Infectious; Oncologic | 19097825; 23522482; 25073507 |
ClinVar
This is a list of variants' phenotypes submitted to
- Severe_combined_immunodeficiency_due_to_CORO1A_deficiency (294 variants)
- Inborn_genetic_diseases (42 variants)
- not_provided (20 variants)
- not_specified (10 variants)
- CORO1A-related_disorder (10 variants)
- Sinoatrial_node_disorder (1 variants)
- Autism_spectrum_disorder (1 variants)
- Severe_combined_immunodeficiency_disease (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CORO1A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007074.4. 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 | 105 | 110 | ||||
| missense | 117 | 123 | ||||
| nonsense | 1 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 11 | |||||
| splice donor/acceptor (+/-2bp) | 4 | |||||
| Total | 7 | 11 | 121 | 108 | 3 |
Highest pathogenic variant AF is 0.00000656996
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CORO1A | protein_coding | protein_coding | ENST00000219150 | 10 | 6250 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.970 | 0.0298 | 125720 | 0 | 5 | 125725 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.48 | 162 | 278 | 0.582 | 0.0000194 | 2956 |
| Missense in Polyphen | 50 | 114.14 | 0.43806 | 1225 | ||
| Synonymous | -1.85 | 140 | 115 | 1.22 | 0.00000794 | 952 |
| Loss of Function | 3.69 | 2 | 19.7 | 0.102 | 0.00000101 | 225 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000582 | 0.0000582 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be a crucial component of the cytoskeleton of highly motile cells, functioning both in the invagination of large pieces of plasma membrane, as well as in forming protrusions of the plasma membrane involved in cell locomotion. In mycobacteria- infected cells, its retention on the phagosomal membrane prevents fusion between phagosomes and lysosomes. {ECO:0000269|PubMed:10338208}.;
- Disease
- DISEASE: Immunodeficiency 8 (IMD8) [MIM:615401]: A disease of the immune system leading to recurrent infections, and characterized by CD4+ T-cells lymphopenia. Patients can develop B-cell lymphoproliferation associated with Epstein-Barr virus infection. {ECO:0000269|PubMed:19097825, ECO:0000269|PubMed:23522482}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Phagosome - Homo sapiens (human);Tuberculosis - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.159
Intolerance Scores
- loftool
- 0.139
- rvis_EVS
- -0.51
- rvis_percentile_EVS
- 21.41
Haploinsufficiency Scores
- pHI
- 0.778
- hipred
- Y
- hipred_score
- 0.698
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.472
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Coro1a
- Phenotype
- endocrine/exocrine gland phenotype; renal/urinary system phenotype; immune system phenotype; cellular phenotype; hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- coro1a
- Affected structure
- pigment cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- immunological synapse formation;phagolysosome assembly;calcium ion transport;phagocytosis;actin filament organization;regulation of cell shape;actin cytoskeleton organization;positive regulation of cell migration;leukocyte chemotaxis;negative regulation of vesicle fusion;cell-substrate adhesion;uropod organization;regulation of actin cytoskeleton organization;nerve growth factor signaling pathway;positive regulation of T cell proliferation;T cell homeostasis;natural killer cell degranulation;negative regulation of neuron apoptotic process;innate immune response;homeostasis of number of cells within a tissue;positive chemotaxis;negative regulation of actin nucleation;regulation of release of sequestered calcium ion into cytosol;early endosome to recycling endosome transport;cellular response to interleukin-4
- Cellular component
- immunological synapse;phagocytic cup;nucleus;cytoplasm;early endosome;cytosol;actin filament;plasma membrane;cell-cell junction;membrane;lamellipodium;axon;phagocytic vesicle membrane;cortical actin cytoskeleton;protein-containing complex;phagocytic vesicle;extracellular exosome;glutamatergic synapse
- Molecular function
- RNA binding;actin binding;actin monomer binding;protein binding;protein C-terminus binding;cytoskeletal protein binding;myosin heavy chain binding;protein homodimerization activity;phosphatidylinositol 3-kinase binding;actin filament binding