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Primary immunodeficiency

Gene: VPS45

Green List (high evidence)

VPS45 (vacuolar protein sorting 45 homolog)
EnsemblGeneIds (GRCh38): ENSG00000136631
EnsemblGeneIds (GRCh37): ENSG00000136631
OMIM: 610035, Gene2Phenotype
VPS45 is in 5 panels

5 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

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): VPS45 .PanelApp HGNC gene symbol check: VPS45 . IUIS Disease: VPS45 deficiency (SCN5) . IUIS Inheritance: AR , .B cells: N/A, .IUIS Other affected cells: N. IUIS Associated features: Extramedullary hematopoiesis, bone marrow fibrosis, nephromegaly . IUIS Major category: Congenital defects of phagocyte number or function. IUIS Subcategory: Congenital Neutropenias
Created: 2 Jul 2018, 10:35 a.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: VPS45, GRID_Gene_Symbol: VPS45, GRID_Transcript_ENS_Community submitted: ENST00000369130, GRID_Transcript_RefSeq: NP_009190.2, GRID_Transcript_ENS_used_on_Production: ENST00000369130
Created: 17 Apr 2018, 12:12 p.m.

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

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

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: Found associated with phenotype in OMIM and not in G2P. Two expert reviewers recommend Green. Found in 1/4 sources. Literature reports two variants in >2 consanguineous Palestinian families
Created: 25 May 2016, 8:26 a.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
  • GRID V2.0
  • Congenital neutropaenia v1.22
Phenotypes
  • Neutropenia, severe congenital, 5, autosomal recessive, 615285
  • Neutropenia, severe congenital 5
  • VPS45 deficiency (SCN5)
  • Extramedullary hematopoiesis, bone marrow fibrosis, nephromegaly
  • Congenital defects of phagocyte number or function
OMIM
610035
Clinvar variants
Variants in VPS45
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 VPS45.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to VPS45.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to VPS45.

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 VPS45 were set to Neutropenia, severe congenital, 5, autosomal recessive, 615285, Neutropenia, severe congenital 5, VPS45 deficiency (SCN5), Extramedullary hematopoiesis, bone marrow fibrosis, nephromegaly, Congenital defects of phagocyte number or function

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to VPS45. 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 VPS45. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: vps45 has been classified as Green List (High Evidence).

13 Jun 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: VPS45 were set to Neutropenia, severe congenital, 5, autosomal recessive, 615285; Neutropenia, severe congenital 5; VPS45 deficiency (SCN5)

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene VPS45 were set to Neutropenia, severe congenital, 5, autosomal recessive, 615285, Neutropenia, severe congenital 5

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to VPS45. Panel: Primary immunodeficiency disorders Phenotypes for gene VPS45 were set to Neutropenia, severe congenital, 5, autosomal recessive, 615285, Neutropenia, severe congenital 5

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

VPS45 was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, Congenital neutropaenia v1.22

29 Mar 2018, Gel status: 4

Created

Louise Daugherty (Genomics England Curator)

VPS45 was created by Louise Daugherty