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Primary immunodeficiency

Gene: STXBP2

Green List (high evidence)

STXBP2 (syntaxin binding protein 2)
EnsemblGeneIds (GRCh38): ENSG00000076944
EnsemblGeneIds (GRCh37): ENSG00000076944
OMIM: 601717, Gene2Phenotype
STXBP2 is in 9 panels

5 reviews

Eleanor Williams (Genomics England Curator)

Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.
Created: 14 Oct 2020, 4:39 p.m. | Last Modified: 14 Oct 2020, 4:39 p.m.
Panel Version: 2.320
Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.
Created: 14 Oct 2020, 4:39 p.m. | Last Modified: 14 Oct 2020, 4:39 p.m.
Panel Version: 2.319
The following PubMed IDs were added to entity STXBP2: 19804848;30557712;22451424;19884660;29776323. These publications have been associated with OMIM phenotype MIM#613101, which is listed for this entity, by the immunedysregulation subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.
Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208

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)

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): STXBP2 .PanelApp HGNC gene symbol check: STXBP2 . IUIS Disease: STXBP2 / Munc18-2 deficiency (FHL5) . IUIS Inheritance: AR or AD .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Fever, HSM, cHLH, cytopenias, enteropathy. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Familial Hemophagocytic Lymphohistiocytosis (FHL syndromes)
Created: 2 Jul 2018, 10:35 a.m.
from GeneReview PMID:20301617: 16% in Central Europeans, Turks, and Saudis (PMID:19804848) and approx 20% in North Americans with FHL PMID:20301617 are FHL5.
Created: 30 Apr 2018, 11:12 a.m.
Changed status from Amber to Green, there are more than 3 unrelated cases to support the phenotype Familial hemophagocytic lymphohistiocytosis-5 (FHL5)caused by homozygous or compound heterozygous mutation in the syntaxin-binding protein-2 gene (STXBP2). From OMIM Publications include: 8 unrelated probands with familial hemophagocytic lymphohistiocytosis (FHL) mapped to STXBP2 in 2 Saudi Arabian and 6 Turkish consanguineous families, zur Stadt et al. (2009) PMID:19804848 sequenced the candidate gene STXBP2 and identified homozygous mutations in STXBP2 in all 8 patients. Also, in affected members of 6 consanguineous families Cote et al. (2009) PMID: 19884660 sequenced the STXBP2 gene and identified homozygosity for the P477L mutation (601717.0001) in 3 Saudi Arabian families and for the IVS14 splice site mutation (601717.0003) in 3 families of Turkish, Palestinian Arab, and Iranian origin, respectively. In PMID: 20798128 Cetica et al. (2010) analyzed the STXBP2 gene in 28 FHL families in which mutations in known FHL genes had been excluded by sequence analysis, and identified homozygosity for 4 different missense mutations in the STXBP2 gene in 4 (14%) of the 28 families, originating from Italy, England, Kuwait, and Pakistan, respectively.
Created: 30 Apr 2018, 11:09 a.m.
Comment on publications: Added publications to support role of STXBP2 variants in Hemophagocytic lymphohistiocytosis, familial, 5
Created: 30 Apr 2018, 10:59 a.m.
From OMIM Familial hemophagocytic lymphohistiocytosis-5 (FHL5) is caused by homozygous or compound heterozygous mutation in the syntaxin-binding protein-2 gene (STXBP2; 601717) on chromosome 19p13.
Created: 30 Apr 2018, 10:55 a.m.
Comment on phenotypes: added OMIM MIMid and synonyms
Created: 30 Apr 2018, 10:49 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: 19 Apr 2018, 1:59 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: STXBP2 (Munc 18-2), PanelApp HGNC gene symbol check: STXBP2, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Diseases of immune dysregulation / Hemophagocytic Lymphohistiocytosis (HLH) / Familial hemophagocytic lymphohistiocytosis syndromes (FHLH)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: STXBP2, GRID_Gene_Symbol: STXBP2, GRID_Transcript_ENS_Community submitted: ENST00000221283, GRID_Transcript_RefSeq: NM_006949.2, GRID_Transcript_ENS_used_on_Production: ENST00000221283
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
  • GOSH PID v.8.0
Phenotypes
  • Hemophagocytic lymphohistiocytosis, familial 5, 613101
  • FHL5
  • Familial hemophagocytic lymphohistiocytosis syndromes (FHLH)
  • Fever, HSM, cHLH, cytopenias, enteropathy
  • Diseases of Immune Dysregulation
OMIM
601717
Clinvar variants
Variants in STXBP2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: stxbp2 has been classified as Green List (High Evidence).

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: stxbp2 has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to STXBP2. Publications for gene STXBP2 were updated from 19804848; 19884660; 20798128; 20301617 to 19884660; 30557712; 29776323; 22451424; 20798128; 20301617; 19804848 Rating Changed from Green List (high evidence) to Red List (low evidence)

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to STXBP2.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to STXBP2.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to STXBP2.

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 STXBP2 were set to Hemophagocytic lymphohistiocytosis, familial 5, 613101, FHL5, Familial hemophagocytic lymphohistiocytosis syndromes (FHLH), Fever, HSM, cHLH, cytopenias, enteropathy, Diseases of Immune Dysregulation

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to STXBP2. 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 STXBP2. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: stxbp2 has been classified as Green List (High Evidence).

30 Apr 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for STXBP2 were set to Hemophagocytic lymphohistiocytosis, familial 5, 613101; FHL5; Familial hemophagocytic lymphohistiocytosis syndromes (FHLH)

30 Apr 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).

30 Apr 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for STXBP2 were set to 19804848; 19884660; 20798128; 20301617

30 Apr 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for STXBP2 were set to Hemophagocytic lymphohistiocytosis, familial, 5,613101; FHL5; Familial hemophagocytic lymphohistiocytosis syndromes (FHLH)

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 STXBP2. Panel: Primary immunodeficiency disorders Phenotypes for gene STXBP2 were set to Hemophagocytic lymphohistiocytosis, familial, 5, Familial hemophagocytic lymphohistiocytosis syndromes (FHLH)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene STXBP2 were set to Hemophagocytic lymphohistiocytosis, familial, 5

17 Apr 2018, Gel status: 1

Added New Source, Set mode of inheritance, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to STXBP2. Panel: Primary immunodeficiency disorders Model of inheritance for gene STXBP2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene STXBP2 were set to Hemophagocytic lymphohistiocytosis, familial, 5

6 Apr 2018, Gel status: 1

Clear Sources

Louise Daugherty (Genomics England Curator)

STXBP2 Source: GOSH PID 20171199 was removed from gene: STXBP2

6 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID v.8.0 was added to STXBP2. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

STXBP2 was added to Primary immunodeficiency disorders panel. Sources: GOSH PID 20171199

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

STXBP2 was created by Louise Daugherty