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Primary immunodeficiency

Gene: LAMTOR2

Green List (high evidence)

LAMTOR2 (late endosomal/lysosomal adaptor, MAPK and MTOR activator 2)
EnsemblGeneIds (GRCh38): ENSG00000116586
EnsemblGeneIds (GRCh37): ENSG00000116586
OMIM: 610389, Gene2Phenotype
LAMTOR2 is in 4 panels

5 reviews

Zornitza Stark (Australian Genomics)

I don't know

Single family reported with some supportive functional data. We have downgraded to Amber on our panel.
Created: 28 Jul 2021, 3:45 a.m. | Last Modified: 28 Jul 2021, 3:45 a.m.
Panel Version: 2.452

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Immunodeficiency due to defect in MAPBP-interacting protein, MIM# 610798

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
neutropenia

Publications

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
Although there is only one large family reported in the literature, the functional evidence is thought to be compelling enough to rate this gene Green
Created: 2 Jul 2018, 1:35 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): LAMTOR2 .PanelApp HGNC gene symbol check: LAMTOR2 . IUIS Disease: P14/LAMTOR2 deficiency . IUIS Inheritance: AR .T cells: Low thymic output, normal in vitro proliferation, .B cells: N/A, .IUIS Other affected cells: N + M. IUIS Associated features: Neutropenia, Hypogammaglobulinemia CD8 cytotoxicity, partial albinism, growth failure . IUIS Major category: Congenital defects of phagocyte number or function. IUIS Subcategory: Congenital Neutropenias
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: Only one pathogenic variant reported in one family. In view of expert review Green, presence on Victorian Clinical Genetics Services panel (2 unrelated cases criteria) and functional info this gene from mouse model this gene was made Green.
Created: 27 Jun 2018, 10:50 a.m.
Comment on publications: added publications on mouse model
Mutated, dysfunctional p14 leads to a human immunodeficiency disorder with endosomal/lysosomal defects in immune cells. Because p14 participates in the regulation of endosomal trafficking, growth factor signaling, and cell proliferation, we investigated the role of p14 in mouse DCs/LCs using a conditional knockout mouse model..p14-mediated disruption of the LAMTOR complex which results in the malfunction of both ERK and mTOR signal pathways. Hence, we conclude that p14 acts as a novel and essential regulator of LC homeostasis in vivo.
Created: 27 Jun 2018, 10:48 a.m.
Comment on publications: To date, it has been described in four members of one Caucasian family, Bohn et al. (2007) PMID: 17195838
Created: 27 Jun 2018, 10:20 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: P14, PanelApp HGNC gene symbol check: LAMTOR2, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Phagocytic disorders / Congenital neutropenia / Congenital neutropenia
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: LAMTOR2, GRID_Gene_Symbol: LAMTOR2, GRID_Transcript_ENS_Community submitted: ENST00000368305, GRID_Transcript_RefSeq: NM_014017.3, GRID_Transcript_ENS_used_on_Production: ENST00000368305
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • North West GLH
  • London North GLH
  • Expert Review Green
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Immunodeficiency due to defect in MAPBP-interacting protein, 610798
  • Congenital neutropenia
  • Primary immunodeficiency syndrome due to p14 deficiency
  • Neutropenia, Hypogammaglobulinemia CD8 cytotoxicity, partial albinism, growth failure
  • Congenital defects of phagocyte number or function
OMIM
610389
Clinvar variants
Variants in LAMTOR2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to LAMTOR2.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to LAMTOR2.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to LAMTOR2.

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.

4 Jul 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: lamtor2 has been classified as Green List (High Evidence).

1 Jul 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene LAMTOR2 were set to Immunodeficiency due to defect in MAPBP-interacting protein, 610798, Congenital neutropenia, Primary immunodeficiency syndrome due to p14 deficiency, Neutropenia, Hypogammaglobulinemia CD8 cytotoxicity, partial albinism, growth failure, Congenital defects of phagocyte number or function

27 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: lamtor2 has been classified as Green List (High Evidence).

27 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: lamtor2 has been classified as Green List (High Evidence).

27 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: LAMTOR2 were set to 17195838; 24092934; 22427693; 28593997

27 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: LAMTOR2 were set to 17195838; 24092934; 22427693

27 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: LAMTOR2 were set to 17195838

27 Jun 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: LAMTOR2 were set to Immunodeficiency due to defect in MAPBP-interacting protein, 610798; Congenital neutropenia; Primary immunodeficiency syndrome due to p14 deficiency

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to LAMTOR2. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to LAMTOR2. Panel: Primary immunodeficiency disorders

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to LAMTOR2. 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 LAMTOR2. Panel: Primary immunodeficiency disorders Phenotypes for gene LAMTOR2 were set to Immunodeficiency due to defect in MAPBP-interacting protein, Congenital neutropenia

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene LAMTOR2 were set to Immunodeficiency due to defect in MAPBP-interacting protein

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

LAMTOR2 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

LAMTOR2 was created by Louise Daugherty