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Primary immunodeficiency

Gene: VPS13B

Green List (high evidence)

VPS13B (vacuolar protein sorting 13 homolog B)
EnsemblGeneIds (GRCh38): ENSG00000132549
EnsemblGeneIds (GRCh37): ENSG00000132549
OMIM: 607817, Gene2Phenotype
VPS13B is in 14 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

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): VPS13B .PanelApp HGNC gene symbol check: VPS13B . IUIS Disease: Cohen syndrome . IUIS Inheritance: AR , .B cells: N/A, .IUIS Other affected cells: N. IUIS Associated features: Dysmorphism, mental retardation, obesity, deafness, neutropenia. IUIS Major category: Congenital defects of phagocyte number or function. IUIS Subcategory: Congenital Neutropenias
Created: 2 Jul 2018, 10:35 a.m.
Comment on publications: Added publications suggested fto support upgrading of the gene to Green
Created: 13 Jun 2018, 1:49 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: COH1, PanelApp HGNC gene symbol check: VPS13B, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Phagocytic disorders / COHEN syndrome / COHEN syndrome
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: VPS13B, GRID_Gene_Symbol: VPS13B, GRID_Transcript_ENS_Community submitted: ENST00000358544, GRID_Transcript_RefSeq: NM_017890.4, GRID_Transcript_ENS_used_on_Production: ENST00000358544
Created: 17 Apr 2018, 12:12 p.m.

Helen Brittain (Genomics England Curator)

Green List (high evidence)

Cyclical neutropaenia is a feature of Cohen syndrome, along with other syndromic associations including retinal dystrophy, ID, obesity.
Created: 19 Sep 2017, 12:07 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Cohen syndrome 216550

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
  • Congenital neutropaenia v1.22
Phenotypes
  • Cohen syndrome, 216550
  • Cohen syndrome
  • Dysmorphism, mental retardation, obesity, deafness, neutropenia
  • Congenital defects of phagocyte number or function
OMIM
607817
Clinvar variants
Variants in VPS13B
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 VPS13B.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to VPS13B.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to VPS13B.

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 VPS13B were set to Cohen syndrome, 216550, Cohen syndrome, Dysmorphism, mental retardation, obesity, deafness, neutropenia, 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 VPS13B. 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 VPS13B. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: vps13b has been classified as Green List (High Evidence).

13 Jun 2018, Gel status: 4

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: VPS13B were set to 12730828; 15154116; 15211651; 20461111; 24311531

20 Apr 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for VPS13B were set to Cohen syndrome, 216550; Cohen syndrome

20 Apr 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for VPS13B were set to Cohen syndrome, 216550; Cohen syndrome

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to VPS13B. Panel: Primary immunodeficiency disorders Phenotypes for gene VPS13B were set to Cohen syndrome 216550, Cohen syndrome, COHEN syndrome

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene VPS13B were set to Cohen syndrome 216550, Cohen syndrome

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to VPS13B. Panel: Primary immunodeficiency disorders Phenotypes for gene VPS13B were set to Cohen syndrome 216550, Cohen syndrome

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

VPS13B 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)

VPS13B was created by Louise Daugherty