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Primary immunodeficiency

Gene: NOD2

Green List (high evidence)

NOD2 (nucleotide binding oligomerization domain containing 2)
EnsemblGeneIds (GRCh38): ENSG00000167207
EnsemblGeneIds (GRCh37): ENSG00000167207
OMIM: 605956, Gene2Phenotype
NOD2 is in 9 panels

7 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, 1:37 p.m. | Last Modified: 14 Oct 2020, 1:37 p.m.
Panel Version: 2.288
The following PubMed IDs were added to entity NOD2: 25416713;28887115;19479837;25136265. These publications have been associated with OMIM phenotype MIM#186580, 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)

Mode of inheritance
Unknown

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with phenotype in OMIM and not in Gen2Phen. At least 6 variants identified in unrelated cases of Blau syndrome 186580.
Created: 9 May 2018, 8:33 a.m.
Comment on phenotypes: Variants also associated with susceptibility to: {Inflammatory bowel disease 1, Crohn disease} 266600, {Psoriatic arthritis, susceptibility to} 607507 and {Yao syndrome} 617321.
Created: 9 May 2018, 8:31 a.m.
Comment on mode of inheritance: Monoallelic inheritance for Blau syndrome 186580.
Created: 9 May 2018, 8:29 a.m.

Sarah Leigh (Genomics England Curator)

Comment on mode of inheritance: Monoallelic inheritance for Blau syndrome 186580.
Created: 9 May 2018, 8:29 a.m.

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): NOD2 (also called CARD15) .PanelApp HGNC gene symbol check: NOD2 . IUIS Disease: Blau syndrome . IUIS Inheritance: AD .T cells: Increased activated T cells, .B cells: N/A, .IUIS Other affected cells: Monocytes. IUIS Associated features: Uveitis, granulomatous synovitis, camptodactyly, rash and cranial neuropathies, 30% develop Crohn colitis. IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Non-Inflammasome Related Conditions
Created: 2 Jul 2018, 10:35 a.m.
Comment on mode of inheritance: added missing MOI from OMIM and Orphanet
Created: 13 Jun 2018, 11:52 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 downloaded from ESID Registry. ESID_Gene_original: CARD15, PanelApp HGNC gene symbol check: NOD2, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Autoinflammatory disorders / Blau syndrome / Caspase recruitment domain-containing protein 15 deficiency (CARD15)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: NOD2, GRID_Gene_Symbol: NOD2, GRID_Transcript_ENS_Community submitted: ENST00000300589, GRID_Transcript_RefSeq: NM_022162.1, GRID_Transcript_ENS_used_on_Production: ENST00000300589
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
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Blau syndrome 186580
  • Caspase recruitment domain-containing protein 15 deficiency (CARD15)
  • Uveitis, granulomatous synovitis, camptodactyly, rash and cranial neuropathies, 30% develop Crohn colitis
  • Autoinflammatory Disorders
OMIM
605956
Clinvar variants
Variants in NOD2
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: nod2 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 NOD2. Publications for gene NOD2 were updated from 11528384; 18955195; 15459013; 4056967 to 11528384; 25416713; 4056967; 25136265; 15459013; 19479837; 18955195; 28887115 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 NOD2.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to NOD2.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to NOD2.

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 NOD2 were set to Blau syndrome 186580, Caspase recruitment domain-containing protein 15 deficiency (CARD15), Uveitis, granulomatous synovitis, camptodactyly, rash and cranial neuropathies, 30% develop Crohn colitis, Autoinflammatory Disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to NOD2. 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 NOD2. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: nod2 has been classified as Green List (High Evidence).

13 Jun 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: NOD2 were set to 11528384; 18955195; 15459013; 4056967

13 Jun 2018, Gel status: 3

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: NOD2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

13 Jun 2018, Gel status: 3

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: NOD2 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

9 May 2018, Gel status: 3

Set publications

Sarah Leigh (Genomics England Curator)

Publications for NOD2 were set to 11528384; 18955195; 15459013

9 May 2018, Gel status: 3

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

9 May 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for NOD2 were set to Blau syndrome 186580; Caspase recruitment domain-containing protein 15 deficiency (CARD15)

9 May 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for NOD2 were set to Blau syndrome 186580; Caspase recruitment domain-containing protein 15 deficiency (CARD15)

9 May 2018, Gel status: 2

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for NOD2 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

9 May 2018, Gel status: 2

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for NOD2 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to NOD2. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to NOD2. Panel: Primary immunodeficiency disorders Phenotypes for gene NOD2 were set to Blau syndrome, Caspase recruitment domain-containing protein 15 deficiency (CARD15)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene NOD2 were set to Blau syndrome

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

NOD2 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

NOD2 was created by Louise Daugherty