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Primary immunodeficiency

Gene: COPA

Green List (high evidence)

COPA (coatomer protein complex subunit alpha)
EnsemblGeneIds (GRCh38): ENSG00000122218
EnsemblGeneIds (GRCh37): ENSG00000122218
OMIM: 601924, Gene2Phenotype
COPA is in 3 panels

5 reviews

Eleanor Williams (Genomics England Curator)

Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.
Created: 14 Oct 2020, 12:39 p.m. | Last Modified: 14 Oct 2020, 12:39 p.m.
Panel Version: 2.239
The following PubMed IDs were added to entity COPA: 25894502. These publications have been associated with OMIM phenotype MIM#616414, which is listed for this entity, by the autoinflammation subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.
Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208

Publications

Kimberly Gilmour (Great Ormond Street Hopsital)

Green List (high evidence)

agree with green gene
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Tracy Briggs (Manchester Genomic Medicine Centre)

Green List (high evidence)

YES- this is covered on our targeted exome
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): COPA .PanelApp HGNC gene symbol check: COPA . IUIS Disease: COPA defect . IUIS Inheritance: AD .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: PMN and tissue specific cells. IUIS Associated features: Autoimmune inflammatory arthritis and interstitial lung disease with Th17 dysregulation and autoantibody production. IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Non-Inflammasome Related Conditions
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: changed rating from Amber to Green, there is enough evidence to support the role of COPA in immune dysfunction
Created: 4 Jun 2018, 1:20 p.m.
added Jensson et al. (2017) PMID:29137621 describe an Icelandic family with three affected individuals over two generations with a rare clinical presentation of lung and joint disease and a histological diagnosis of follicular bronchiolitis. This is the second report of the p.Glu241Lys mutation in COPA, indicating the recurrent nature of the mutation. The mutation was reported to co-segregate with COPA syndrome in a large family from the USA with five affected members, and classified as pathogenic. The two separate occurrences of the p.Glu241Lys mutation in cases and its absence from a large number of sequenced genomes confirms its role in the pathogenesis of the COPA syndrome.
Created: 4 Jun 2018, 1:18 p.m.
Comment on publications: added Noorelahi et al. (2018) PMID: 28956095 describe a 12-year-old boy presenting with dyspnea on exertion, fatigue and clubbing. Additional findings included a restrictive pattern of pulmonary involvement and positive inflammatory markers and autoantibodies. Genetic testing revealed a p.W240R variant of the COPA gene confirming the diagnosis of Copa syndrome.
Created: 4 Jun 2018, 1:08 p.m.
added missense-tag. Currently only missense variants have been reported
Created: 4 Jun 2018, 1:02 p.m.
Comment on publications: added publications to support COPA mutations impair ER-Golgi transport and cause hereditary autoimmune-mediated lung disease and arthritis.
Created: 4 Jun 2018, 12:59 p.m.
from Watkin et al. (2015) i PMID: 25894502 In 30 individuals from 5 unrelated families with Autoimmune interstitial lung, joint, and kidney disease identified 4 different heterozygous missense mutations in the COPA gene (601924.0001-601924.0004). All mutations affected the WD40 domain. Nine mutation carriers were clinically unaffected, consistent with incomplete penetrance. It has been indicated that the variants contribute to susceptibility susceptibility to infection.
Created: 4 Jun 2018, 12:46 p.m.
COPA syndrome is an autoinflammatory disease that presents as pulmonary hemosiderosis and polyarticular arthritis. COPA gene encodes a subunit of the coatomer protein complex (COPI), a carrier complex required for retrograde protein trafficking from the Golgi to the endoplasmic reticulum (ER)
Created: 4 Jun 2018, 11:24 a.m.
Comment on phenotypes: added MIMid from OMIM and phenotype from Orphanet
Created: 4 Jun 2018, 11:21 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 20 Apr 2018, 12:25 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: COPA, GRID_Gene_Symbol: COPA, GRID_Transcript_ENS_Community submitted: ENST00000368069, GRID_Transcript_RefSeq: NM_001098398.1, GRID_Transcript_ENS_used_on_Production: ENST00000368069
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • GRID V2.0
Phenotypes
  • Autoimmune inflammatoy arthritis and interstial lung disease, 616414
  • Autoimmune interstitial lung disease-arthritis syndrome
  • COPA syndrome
  • Autoimmune inflammatory arthritis and interstitial lung disease with Th17 dysregulation and autoantibody production
  • Autoinflammatory Disorders
Tags
missense
OMIM
601924
Clinvar variants
Variants in COPA
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: copa has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to COPA. Publications for gene COPA were updated from 25894502; 28956095; 25894502; 29137621 to 28956095; 25894502; 29137621 Rating Changed from Green List (high evidence) to Red List (low evidence)

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to COPA.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to COPA.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to COPA.

12 Jul 2018, Gel status: 4

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

1 Jul 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene COPA were set to Autoimmune inflammatoy arthritis and interstial lung disease, 616414, Autoimmune interstitial lung disease-arthritis syndrome, COPA syndrome, Autoimmune inflammatory arthritis and interstitial lung disease with Th17 dysregulation and autoantibody production, Autoinflammatory Disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to COPA. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to COPA. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: copa has been classified as Green List (High Evidence).

4 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: copa has been classified as Green List (High Evidence).

4 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: COPA were set to 25894502; 28956095; 25894502; 29137621

4 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: COPA were set to 25894502; 28956095; 25894502

4 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: COPA were set to 25894502,28956095

4 Jun 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: COPA were set to Autoimmune inflammatoy arthritis and interstial lung disease, 616414; Autoimmune interstitial lung disease-arthritis syndrome; COPA syndrome

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to COPA. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene COPA were set to Autoimmune inflammatoy arthritis and interstial lung disease

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

COPA was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

COPA was created by Louise Daugherty