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Primary immunodeficiency

Gene: TRNT1

Green List (high evidence)

TRNT1 (tRNA nucleotidyl transferase 1)
EnsemblGeneIds (GRCh38): ENSG00000072756
EnsemblGeneIds (GRCh37): ENSG00000072756
OMIM: 612907, Gene2Phenotype
TRNT1 is in 12 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): TRNT1 .PanelApp HGNC gene symbol check: TRNT1 . IUIS Disease: TRNT1 deficiency . IUIS Inheritance: AR .T cells: Decreased or normal,, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: congenital sideroblastic anemia, deafness, developmental delay. IUIS Major category: Predominantly Antibody Deficiencies. IUIS Subcategory: Severe Reduction in at Least 2 Serum Immunoglobulin Isotypes with Normal or Low Number of B Cells, CVID Phenotype
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: Changed Amber to Green from external expert review and further publications to support gene-disease association
Created: 27 Jun 2018, 6:59 p.m.
Comment on publications: Added publication to support gene-disease association. More than three pathogenic variants found more than three unrelated cases.
Created: 27 Jun 2018, 6:58 p.m.
from Orphanet: congenital sideroblastic anemia -B cell immunodeficiency- periodic fever-developmental delay syndrome is a form of constitutional sideroblastic anemia (see this term), characterized by severe microcytic anemia, B-cell lymphopenia , panhypogammaglobulinemia and variable neurodegeneration. The disease presents in infancy with recurrent febrile illnesses, gastrointestinal disturbances, developmental delay, seizures, ataxia and sensorineural deafness. Most patients require regular blood transfusion, iron chelation, and intravenous immunoglobulin (IVIG) replacement. Stem cell transplantation has been reported to be successful.
Created: 27 Jun 2018, 6:57 p.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: 19 Apr 2018, 11:10 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: TNRT1, PanelApp HGNC gene symbol check: TRNT1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / Congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD) / Congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: TRNT1, GRID_Gene_Symbol: TRNT1, GRID_Transcript_ENS_Community submitted: ENST00000251607, GRID_Transcript_RefSeq: NM_001302946.1, GRID_Transcript_ENS_used_on_Production: ENST00000251607
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
  • Congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD)
  • Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay, 616084
  • congenital sideroblastic anemia, deafness, developmental delay
  • Predominantly Antibody Deficiencies
OMIM
612907
Clinvar variants
Variants in TRNT1
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 TRNT1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to TRNT1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to TRNT1.

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 TRNT1 were set to Congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD), Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay, 616084, congenital sideroblastic anemia, deafness, developmental delay, Predominantly Antibody Deficiencies

27 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: trnt1 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: trnt1 has been classified as Green List (High Evidence).

27 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: TRNT1 were set to 23553769; 29055896; 25193871

27 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: TRNT1 were set to 23553769; 29055896; 25193871

27 Jun 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: TRNT1 were set to Congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD); Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay, 616084

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to TRNT1. 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 TRNT1. Panel: Primary immunodeficiency disorders

20 Apr 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for TRNT1 were set to Congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD)

19 Apr 2018, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to TRNT1. Panel: Primary immunodeficiency disorders Phenotypes for gene TRNT1 were set to congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD), Congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene TRNT1 were set to congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD)

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

TRNT1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

TRNT1 was created by Louise Daugherty