Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: TCN2Comment 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, 4:41 p.m. | Last Modified: 14 Oct 2020, 4:41 p.m.
Panel Version: 2.323
The following PubMed IDs were added to gene TCN2 (OMIM gene MIM#613441): 7849710;19373259;12107818. These publications have been associated with the gene by the immunodeficiencies 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
agree with green geneCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
YES- this is covered on our targeted exomeCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
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): TCN2 .PanelApp HGNC gene symbol check: TCN2 . IUIS Disease: Transcobalamin 2 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Variable, .IUIS Other affected cells: N/A. IUIS Associated features: Megaloblastic anemia, pancytopenia, if untreated for prolonged periods results in intellectual disability. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Defects of Vitamin B12 and Folate MetabolismCreated: 2 Jul 2018, 10:35 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: TCN2, PanelApp HGNC gene symbol check: TCN2, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / Defects of Vitamin B12 and Folate metabolism / Defects of Vitamin B12 and Folate metabolism; Predominantly antibody disorders / Hypogammaglobulinemias / Transcobalamin II deficiencyCreated: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: TCN2, GRID_Gene_Symbol: TCN2, GRID_Transcript_ENS_Community submitted: ENST00000215838, GRID_Transcript_RefSeq: NM_000355.2, GRID_Transcript_ENS_used_on_Production: ENST00000215838Created: 17 Apr 2018, 12:12 p.m.
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Comment when marking as ready: two green expert reviews and many publicationsCreated: 10 May 2016, 12:42 p.m.
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Transcobalamin II deficiency; can have a presentation similar to severe combined immunodeficiency; pancytopenia; neutropenic colitis; Agammaglobulinemia; megaloblastic bone marrow; thrombocytopenia; neutropenia; failure to thrive; hypotonia, myoclonic like movements, pallor, purpura, anaemia, thrombocytopenia, megaloblastosis, aplastic bone marrow.
Publications
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Publications
Comment when marking as ready: Gene added by a reviewer, and rated green by two reviewers. Ready for Version 1.Created: 17 Dec 2015, 10:58 a.m.
Gene: tcn2 has been classified as Green List (High Evidence).
Source Other was added to TCN2. Publications for gene TCN2 were updated from 24305960; 7980584; 7849710; 20352340; 18956254 to 18956254; 20352340; 7849710; 7980584; 12107818; 19373259; 24305960 Rating Changed from Green List (high evidence) to Red List (low evidence)
Source NHS GMS was added to TCN2.
Source North West GLH was added to TCN2.
Source London North GLH was added to TCN2.
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.
Phenotypes for gene TCN2 were set to Transcobalamin II deficiency, 275350, Transcobalamin II deficiency, can have a presentation similar to severe combined immunodeficiency, pancytopenia, neutropenic colitis, Agammaglobulinemia, megaloblastic bone, Transcobalamin-2 precursor, Defects of Vitamin B12 and Folate metabolism, Megaloblastic anemia, pancytopenia, if untreated for prolonged periods results in intellectual disability, Combined immunodeficiencies with associated or syndromic features
IUIS Classification February 2018 was added to TCN2. Panel: Primary immunodeficiency disorders
Victorian Clinical Genetics Services was added to TCN2. Panel: Primary immunodeficiency disorders
Gene: tcn2 has been classified as Green List (High Evidence).
ESID Registry 20171117 was added to TCN2. Panel: Primary immunodeficiency disorders Phenotypes for gene TCN2 were set to Transcobalamin II deficiency, 275350, Transcobalamin II deficiency, can have a presentation similar to severe combined immunodeficiency, pancytopenia, neutropenic colitis, Agammaglobulinemia, megaloblastic bone, Transcobalamin-2 precursor, Defects of Vitamin B12 and Folate metabolism
Phenotypes for gene TCN2 were set to Transcobalamin II deficiency, 275350, Transcobalamin II deficiency, can have a presentation similar to severe combined immunodeficiency, pancytopenia, neutropenic colitis, Agammaglobulinemia, megaloblastic bone, Transcobalamin-2 precursor
GRID V2.0 was added to TCN2. Panel: Primary immunodeficiency disorders Phenotypes for gene TCN2 were set to Transcobalamin II deficiency, 275350, Transcobalamin II deficiency, can have a presentation similar to severe combined immunodeficiency, pancytopenia, neutropenic colitis, Agammaglobulinemia, megaloblastic bone, Transcobalamin-2 precursor
Phenotypes for TCN2 were set to Transcobalamin II deficiency, 275350; Transcobalamin II deficiency; can have a presentation similar to severe combined immunodeficiency; pancytopenia; neutropenic colitis; Agammaglobulinemia; megaloblastic bone
Phenotypes for TCN2 were set to Transcobalamin II deficiency, 275350
Publications for TCN2 were set to 24305960; 7980584; 7849710; 20352340; 18956254
Publications for TCN2 were set to 24305960; 7849710; 20352340; 18956254; 24305960; 20352340
Publications for TCN2 were set to 24305960; 7849710; 20352340; 18956254; 24305960; 7980584; 7849710; 20352340
Publications for TCN2 were set to 24305960; 7980584; 7849710; 20352340; 18956254; 24305960; 7980584; 7849710; 20352340
Congenital neutropaenia v1.22 was added to TCN2. Panel: Primary immunodeficiency disorders Publications for gene TCN2 was set to ['24305960', '7980584', '7849710', '20352340', '18956254', '18956254 ']
SCID v1.6 was added to TCN2. Panel: Primary immunodeficiency disorders
Combined B and T cell defect v1.12 was added to TCN2. Panel: Primary immunodeficiency disorders Publications for gene TCN2 was set to ['24305960', '7980584', '7849710', '20352340', '18956254 ']
Agranulocytosis v1.3 was added to TCN2. Panel: Primary immunodeficiency disorders Publications for gene TCN2 was set to ['24305960', ' 7980584', ' 7849710', ' 20352340', ' 18956255']
TCN2 was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, A- or hypo-gammaglobulinaemia v1.25
TCN2 was created by Louise Daugherty