CORO1A

coronin 1A, the group of WD repeat domain containing|Coronins

Basic information

Region (hg38): 16:30182827-30189076

Links

ENSG00000102879 ∙ NCBI:11151 ∙ OMIM:605000 ∙ HGNC:2252 ∙ Uniprot:P31146 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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: CGD

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 ClinVar and linked to the CORO1A gene.

• Severe combined immunodeficiency due to CORO1A deficiency (5 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.

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	91	4	97
missense		1	92	2		95
nonsense	1					1
start loss						0
frameshift	4	1	1			6
inframe indel			1			1
splice donor/acceptor (+/-2bp)		3	1			4
splice region			6	15		21
non coding			3	45	5	53
Total	5	5	100	138	9

Highest pathogenic variant AF is 0.00000657

Variants in CORO1A

This is a list of pathogenic ClinVar variants found in the CORO1A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30183126-A-C		not specified	Benign (Jan 24, 2024)
16-30185228-C-T		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (Jun 16, 2023)
16-30185232-C-T		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (Aug 31, 2021)
16-30185244-G-T		Severe combined immunodeficiency due to CORO1A deficiency	Likely pathogenic (May 20, 2022)
16-30185248-C-T		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (Sep 29, 2023)
16-30185251-G-C		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Aug 04, 2021)
16-30185263-G-A		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Dec 06, 2022)
16-30185263-G-C		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Jul 28, 2023)
16-30185266-C-T		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Feb 10, 2022)
16-30185272-C-A		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Dec 19, 2023)
16-30185291-G-A		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (Feb 20, 2022)
16-30185296-C-T		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Nov 14, 2022)
16-30185312-T-C		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (Apr 20, 2022)
16-30185337-A-G		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (Sep 19, 2022)
16-30185338-C-T		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Dec 18, 2023)
16-30185356-G-A		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Dec 19, 2023)
16-30185395-G-C		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Oct 20, 2023)
16-30185394-T-TGCCCCTGGGCAAGGTGA		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (May 04, 2022)
16-30185395-G-GCC		Sinoatrial node disorder	Likely pathogenic (May 06, 2022)
16-30185397-C-G		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (Apr 07, 2022)
16-30185410-G-A		Severe combined immunodeficiency due to CORO1A deficiency	Uncertain significance (Aug 08, 2022)
16-30185420-G-C		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Nov 23, 2022)
16-30185424-C-T		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Mar 22, 2022)
16-30185427-G-C		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Oct 05, 2023)
16-30186578-A-T		Severe combined immunodeficiency due to CORO1A deficiency	Likely benign (Jun 24, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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