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Primary immunodeficiency

Gene: ATM

Green List (high evidence)

ATM (ATM serine/threonine kinase)
EnsemblGeneIds (GRCh38): ENSG00000149311
EnsemblGeneIds (GRCh37): ENSG00000149311
OMIM: 607585, Gene2Phenotype
ATM is in 29 panels

4 reviews

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): ATM .PanelApp HGNC gene symbol check: ATM . IUIS Disease: Ataxia-telangiectasia . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: DNA Repair Defects other than those listed in Table 1
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: changed from Amber to Green after internal clinical review. It was felt there is probably a sufficient immunological phenotype to make this disorder relevant to this panel, accepting that there is an associated cancer risk. If a diagnosis is made, this will make a difference to cancer treatment options / screening in view of the risks and sensitivity to ionising radiation.
Created: 11 May 2018, 3:36 p.m.
Comment on publications: added PMID:27884168 (2016) review
Created: 11 May 2018, 12:13 p.m.
To be discussed with clinical team as to whether this is further demoted to Red. Enough cases and PID relevant but Ataxia-telangiectasia is associated to increased risk to cancer
Created: 11 May 2018, 12:04 p.m.
Comment on phenotypes: added PID phenotype
Created: 11 May 2018, 11:59 a.m.
from orphanet: Ataxia-telangiectasia is the association of severe combined immunodeficiency (affecting mainly the humoral immune response) with progressive cerebellar ataxia. It is characterised by neurological signs, telangiectasias, increased susceptibility to infections and a higher risk of cancer.
Created: 11 May 2018, 11:58 a.m.
Comment on phenotypes: added OMIM MIMid
Created: 11 May 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: ATM, PanelApp HGNC gene symbol check: ATM, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / DNA-breakage disorder / Ataxia telangiectasia (ATM)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: ATM, GRID_Gene_Symbol: ATM, GRID_Transcript_ENS_Community submitted: ENST00000278616, GRID_Transcript_RefSeq: NM_000051.3, GRID_Transcript_ENS_used_on_Production: ENST00000278616
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
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • Expert Review Green
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Ataxia-telangiectasia, OMIM:208900
  • Combined immunodeficiencies with associated or syndromic features
  • Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations
OMIM
607585
Clinvar variants
Variants in ATM
Penetrance
None
Publications
Panels with this gene

History Filter Activity

15 Jul 2021, Gel status: 3

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: ATM were changed from Ataxia-telangiectasia, 208900; Ataxia telangiectasia (ATM); immunodeficiency; Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations; Combined immunodeficiencies with associated or syndromic features to Ataxia-telangiectasia, OMIM:208900; Combined immunodeficiencies with associated or syndromic features; Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to ATM.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to ATM.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to ATM.

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 ATM were set to Ataxia-telangiectasia, 208900, Ataxia telangiectasia (ATM), immunodeficiency, Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

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

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

11 May 2018, Gel status: 3

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

11 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for ATM were set to 27884168; 2005780; 2136770; 7792600; 27421701

11 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for ATM were set to Ataxia-telangiectasia, 208900; Ataxia telangiectasia (ATM); immunodeficiency

11 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for ATM were set to Ataxia-telangiectasia, 208900; Ataxia telangiectasia (ATM); immunodeficiency

11 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for ATM were set to Ataxia-telangiectasia, 208900; Ataxia telangiectasia (ATM)

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to ATM. 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 ATM. Panel: Primary immunodeficiency disorders Phenotypes for gene ATM were set to Ataxia-telangiectasia, Ataxia telangiectasia (ATM)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene ATM were set to Ataxia-telangiectasia

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

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

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

ATM was created by Louise Daugherty