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Primary immunodeficiency

Gene: ACP5

Green List (high evidence)

ACP5 (acid phosphatase 5, tartrate resistant)
EnsemblGeneIds (GRCh38): ENSG00000102575
EnsemblGeneIds (GRCh37): ENSG00000102575
OMIM: 171640, Gene2Phenotype
ACP5 is in 10 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, 12:21 p.m. | Last Modified: 14 Oct 2020, 12:21 p.m.
Panel Version: 2.217
The following PubMed IDs were added to entity ACP5: 26951490. These publications have been associated with OMIM phenotype MIM#607944, which is listed for this entity, by the autoinflammation 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): ACP5 .PanelApp HGNC gene symbol check: ACP5 . IUIS Disease: Spondyloenchondro-dysplasia with immune dysregulation (SPENCD) . IUIS Inheritance: AR .T cells: Normal, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Short stature, SP, ICC, SLE, thrombocytopenia and autoimmune hemolytic anemia, possibly recurrent bacterial and viral infections . IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Type 1 Interferonopathies
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: Changed status from Amber to Green, there are more than 3 unrelated cases to support the PID phenotype
Created: 30 Apr 2018, 1:58 p.m.
Comment on publications: Added publications to support the phenotype. From OMIM: In 10 patients (8 families) with spondyloenchondrodysplasia with immune dysregulation (SPENCDI) Briggs et al. (2011) PMID: 21217755 identified homozygosity or compound heterozygosity for mutations in the ACP5. In vivo testing confirmed a loss of expressed protein, and all 8 cases assayed showed elevated serum interferon alpha activity, with gene expression profiling in whole blood defining a type I interferon signature. Also Lausch et al. (2011) PMID:21217752 mapped SPENCDI to chromosome 19p13 and identified homozygous or compound heterozygous mutations in the ACP5 gene in 14 affected individuals from 11 families, they also demonstrated that the mutations abolished TRAP enzyme function in serum and cells of affected individuals, and that phosphorylated osteopontin accumulated in serum, urine, and cells cultured from TRAP-deficient individuals. Case-derived dendritic cells exhibited an altered cytokine profile and were more potent than matched controls in stimulating allogeneic T-cell proliferation in mixed lymphocyte reactions. In a girl who had severe immune dysregulation with neurologic impairment and only minor bone changes, Girschick et al. (2015) PMID: 26346816 identified compound heterozygosity for a missense mutation and a 1-bp duplication in the ACP5 gene. The authors concluded that mutation in ACP5 can cause severe immune dysregulation and neurologic impairment even in the absence of metaphyseal dysplasia. In a Turkish sister and brother exhibiting spondyloenchondrodysplasia without immune dysregulation or neurologic abnormalities, de Bruin et al. (2016) PMID:26789720 performed exome sequencing and identified homozygosity for a frameshift mutation in the ACP5 gene
Created: 30 Apr 2018, 1:56 p.m.
It is a confirmed DD gene for Spondyloenchondrodysplasia with immune dysregulation, which includes CNS calcifications. More than 3 families reported in the publications provided.
Created: 30 Apr 2018, 1:41 p.m.
from OMIM: Spondyloenchondrodysplasia with immune dysregulation is an immunoosseous dysplasia combining the typical metaphyseal and vertebral bone lesions of spondyloenchondrodysplasia with immune dysfunction and neurologic involvement.
Created: 30 Apr 2018, 1:39 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: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: ACP5, PanelApp HGNC gene symbol check: ACP5, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Diseases of immune dysregulation / Type 1 interferonopathies / Type 1 interferonopathies
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: ACP5, GRID_Gene_Symbol: ACP5, GRID_Transcript_ENS_Community submitted: ENST00000592828, GRID_Transcript_RefSeq: NM_001111034.2, GRID_Transcript_ENS_used_on_Production: ENST00000592828
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
Phenotypes
  • Spondyloenchondrodysplasia with immune dysregulation Type 1 interferonopathies
  • Spondyloenchondrodysplasia with immune dysregulation, 607944
  • Type 1 interferonopathies
  • Short stature, SP, ICC, SLE, thrombocytopenia and autoimmune hemolytic anemia, possibly recurrent bacterial and viral infections
  • Autoinflammatory Disorders
OMIM
171640
Clinvar variants
Variants in ACP5
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: acp5 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 ACP5. Publications for gene ACP5 were updated from 26789720; 26951490; 26346816; 18924170; 21217755; 26789720; 21217752 to 21217755; 26789720; 21217752; 18924170; 26951490; 26346816 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 ACP5.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to ACP5.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to ACP5.

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 ACP5 were set to Spondyloenchondrodysplasia with immune dysregulation Type 1 interferonopathies, Spondyloenchondrodysplasia with immune dysregulation, 607944, Type 1 interferonopathies, Short stature, SP, ICC, SLE, thrombocytopenia and autoimmune hemolytic anemia, possibly recurrent bacterial and viral infections, Autoinflammatory Disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to ACP5. 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 ACP5. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: acp5 has been classified as Green List (High Evidence).

9 May 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for ACP5 were set to Spondyloenchondrodysplasia with immune dysregulation Type 1 interferonopathies; Spondyloenchondrodysplasia with immune dysregulation, 607944; Type 1 interferonopathies

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 ACP5 were set to 26789720; 26951490; 26346816; 18924170; 21217755; 26789720; 21217752

30 Apr 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for ACP5 were set to Spondyloenchondrodysplasia with immune dysregulation Type 1 interferonopathies; Spondyloenchondrodysplasia with immune dysregulation, 607944

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to ACP5. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to ACP5. Panel: Primary immunodeficiency disorders Phenotypes for gene ACP5 were set to Spondyloenchondrodysplasia with immune dysregulation, Type 1 interferonopathies

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene ACP5 were set to Spondyloenchondrodysplasia with immune dysregulation

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

ACP5 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

ACP5 was created by Louise Daugherty