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Primary immunodeficiency

Gene: XIAP

Green List (high evidence)

XIAP (X-linked inhibitor of apoptosis)
EnsemblGeneIds (GRCh38): ENSG00000101966
EnsemblGeneIds (GRCh37): ENSG00000101966
OMIM: 300079, Gene2Phenotype
XIAP is in 6 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

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, 4:47 p.m. | Last Modified: 14 Oct 2020, 4:47 p.m.
Panel Version: 2.332
The following PubMed IDs were added to entity XIAP: 31754776;23973892;21119115;26581487;23131490. These publications have been associated with OMIM phenotype MIM#300635, 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
Comment on publications: Adding publications from reviewer and OMIM
Created: 20 Jun 2018, 9:16 a.m.
XIAP is associated with Lymphoproliferative syndrome, X-linked, 2 in OMIM. This is an X-linked primary immune deficiency. OMIM report multiple cases of variants in the XIAP gene being associated with Lymphoproliferative syndrome, X-linked in Rigaud et al. (2006) (PMID: 17080092), Worthey et al. (2011) (PMID: 21173700), Yang et al. (2012) (PMID: 22228567), Dziadzio et al (2015) (PMID: 25943627). From these four studies 11 families were examined. Variant change effects include hemizygous frameshift, nonsense, missense and deletion mutations. The family described in Dziadzio et al (2015) includes female carriers with random X-inactivation which led to inflammatory symptoms.
Created: 20 Jun 2018, 9:13 a.m.

Publications

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

Phenotypes
haemophagocytic lymphohistiocytosis; inflammatory bowel disease; splenomegaly

Publications

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): XIAP .PanelApp HGNC gene symbol check: XIAP . IUIS Disease: XIAP deficiency (XLP2) . IUIS Inheritance: XL , .B cells: Normal or reduced Memory B cells, .IUIS Other affected cells: N/A. IUIS Associated features: EBV infection, Splenomegaly, lymphoproliferation, HLH, Colitis, IBD, hepatitis, Low iNKT cells, hypogammaglobulinemia. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Susceptibility to EBV and Lymphoproliferative Conditions
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: Changed Amber to Green from external review comment and further publications to support gene-disease association
Created: 20 Jun 2018, 9:31 p.m.
Comment on phenotypes: Added phenotypes suggested from external expert review.
Created: 20 Jun 2018, 9:25 p.m.
Comment on mode of inheritance: Added MOI from external expert review (changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females)
Created: 20 Jun 2018, 9:24 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, 10:30 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: BIRC4/XIAP (XLP2), PanelApp HGNC gene symbol check: XIAP, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Diseases of immune dysregulation / Hemophagocytic Lymphohistiocytosis (HLH) / X-linked lymphoproliferative syndrome (XLP)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: XIAP, GRID_Gene_Symbol: XIAP, GRID_Transcript_ENS_Community submitted: ENST00000371199, GRID_Transcript_RefSeq: NM_001167.3, GRID_Transcript_ENS_used_on_Production: ENST00000371199
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
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
  • Lymphoproliferative syndrome, X-linked, 2
  • 300635
  • Lymphoproliferative syndrome, X-linked, 2 (XLP2)
  • X-linked lymphoproliferative syndrome (XLP)
  • haemophagocytic lymphohistiocytosis
  • inflammatory bowel disease
  • splenomegaly
  • EBV infection, Splenomegaly, lymphoproliferation, HLH, Colitis, IBD, hepatitis, Low iNKT cells, hypogammaglobulinemia
  • Diseases of Immune Dysregulation
OMIM
300079
Clinvar variants
Variants in XIAP
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: xiap 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 XIAP. Publications for gene XIAP were updated from 17080092; 21119115; 25943627; 21173700; 22228567 to 26581487; 21119115; 23973892; 17080092; 21173700; 22228567; 23131490; 25943627; 31754776 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 XIAP.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to XIAP.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to XIAP.

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 XIAP were set to Lymphoproliferative syndrome, X-linked, 2, 300635, Lymphoproliferative syndrome, X-linked, 2 (XLP2), X-linked lymphoproliferative syndrome (XLP), haemophagocytic lymphohistiocytosis, inflammatory bowel disease, splenomegaly, EBV infection, Splenomegaly, lymphoproliferation, HLH, Colitis, IBD, hepatitis, Low iNKT cells, hypogammaglobulinemia, 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 XIAP. 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 XIAP. Panel: Primary immunodeficiency disorders

20 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

20 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

20 Jun 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: XIAP were set to Lymphoproliferative syndrome, X-linked, 2; 300635; Lymphoproliferative syndrome, X-linked, 2 (XLP2); X-linked lymphoproliferative syndrome (XLP); haemophagocytic lymphohistiocytosis; inflammatory bowel disease; splenomegaly

20 Jun 2018, Gel status: 2

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: XIAP was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

20 Jun 2018, Gel status: 2

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene: XIAP were set to 17080092; 21119115; 25943627; 21173700; 22228567

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 XIAP. Panel: Primary immunodeficiency disorders Phenotypes for gene XIAP were set to Lymphoproliferative syndrome, X-linked, 2, Lymphoproliferative syndrome, X-linked, 2 (XLP2), X-linked lymphoproliferative syndrome (XLP)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene XIAP were set to Lymphoproliferative syndrome, X-linked, 2, Lymphoproliferative syndrome, X-linked, 2 (XLP2)

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 XIAP. Panel: Primary immunodeficiency disorders Model of inheritance for gene XIAP was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene XIAP were set to Lymphoproliferative syndrome, X-linked, 2, Lymphoproliferative syndrome, X-linked, 2 (XLP2)

6 Apr 2018, Gel status: 1

Clear Sources

Louise Daugherty (Genomics England Curator)

XIAP Source: GOSH PID 20171208 was removed from gene: XIAP

6 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

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

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

XIAP was added to Primary immunodeficiency disorders panel. Sources: GOSH PID 20171208

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

XIAP was created by Louise Daugherty