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Primary immunodeficiency

Gene: CARMIL2

Green List (high evidence)

CARMIL2 (capping protein regulator and myosin 1 linker 2)
EnsemblGeneIds (GRCh38): ENSG00000159753
EnsemblGeneIds (GRCh37): ENSG00000159753
OMIM: 610859, Gene2Phenotype
CARMIL2 is in 3 panels

6 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, 12:27 p.m. | Last Modified: 14 Oct 2020, 12:27 p.m.
Panel Version: 2.227
The following PubMed IDs were added to gene CARMIL2 (OMIM gene MIM#610859): 27647349;28112205;29479355. These publications have been associated with the gene by the immunedysregulation 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
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
combined immunodeficiency; EBV+ disseminated smooth muscle tumours

Publications

Sarah Leigh (Genomics England Curator)

Comment on list classification: Not associated with phenotype in OMIM or in Gen2Phen. PMID 27896283 reports 4 Norwegian cases from three families who had the same variant (p.Leu639His) together together with a shared haplotype.
Created: 9 May 2018, 3:34 p.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): RLTPR .PanelApp HGNC gene symbol check: CARMIL2 . IUIS Disease: RLTPR (CARMIL2) deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Nl number, .IUIS Other affected cells: N/A. IUIS Associated features: Recurrent bacterial, fungal and mycobacterial infections, viral warts, molluscum and EBV lymphoproliferative and other malignancy, atopy. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Susceptibility to EBV and Lymphoproliferative Conditions
Created: 2 Jul 2018, 10:35 a.m.
Comment on phenotypes: Added phenotypes suggested from external expert review.
Created: 12 Jun 2018, 10:48 a.m.
Comment on publications: Added publications suggested from external expert review to support upgrading of the gene to Green
Created: 12 Jun 2018, 10:48 a.m.
removed founder tag- different variants (and consequences) have been found in other populations not just of Norwegian origin. PMID:27647349 and 28112205
Created: 12 Jun 2018, 10:46 a.m.
Comment on list classification: Changed Red to Green from external review comment and further publications to support there are more than three unrelated families with combined immunodeficiency; EBV+ disseminated smooth muscle tumours
Created: 12 Jun 2018, 10:41 a.m.
previous HGNC gene symbol for CARMIL2 was RLTPR
Created: 12 Jun 2018, 10:26 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: RLTPR, PanelApp HGNC gene symbol check: CARMIL2, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency
Created: 17 Apr 2018, 12:29 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • ESID Registry 20171117
Phenotypes
  • Combined immunodeficiency
  • warts, molluscum contagiosum, and T‐cell dysfunction
  • EBV+ disseminated smooth muscle tumours
  • Recurrent bacterial, fungal and mycobacterial infections, viral warts, molluscum and EBV lymphoproliferative and other malignancy, atopy
  • Diseases of Immune Dysregulation
OMIM
610859
Clinvar variants
Variants in CARMIL2
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: carmil2 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 CARMIL2. Publications for gene CARMIL2 were updated from 27896283; 27647349; 28112205 to 27647349; 27896283; 28112205; 29479355 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 CARMIL2.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to CARMIL2.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to CARMIL2.

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 CARMIL2 were set to Combined immunodeficiency, warts, molluscum contagiosum, and T‐cell dysfunction, EBV+ disseminated smooth muscle tumours, Recurrent bacterial, fungal and mycobacterial infections, viral warts, molluscum and EBV lymphoproliferative and other malignancy, atopy, Diseases of Immune Dysregulation

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to CARMIL2. Panel: Primary immunodeficiency disorders

12 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: carmil2 has been classified as Green List (High Evidence).

12 Jun 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: CARMIL2 were set to Combined immunodeficiency; warts, molluscum contagiosum, and T‐cell dysfunction; EBV+ disseminated smooth muscle tumours

12 Jun 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: CARMIL2 were set to 27896283; 27647349; 28112205

12 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: carmil2 has been classified as Green List (High Evidence).

9 May 2018, Gel status: 1

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

9 May 2018, Gel status: 1

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for CARMIL2 was changed from to BIALLELIC, autosomal or pseudoautosomal

9 May 2018, Gel status: 1

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for CARMIL2 were set to Combined immunodeficiency; warts, molluscum contagiosum, and T‐cell dysfunction

9 May 2018, Gel status: 1

Set publications

Sarah Leigh (Genomics England Curator)

Publications for CARMIL2 were set to 27896283

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

CARMIL2 was added to Primary immunodeficiency disorders panel. Sources: ESID Registry 20171117

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

CARMIL2 was created by Louise Daugherty