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Primary immunodeficiency

Gene: APOL1

Red List (low evidence)

APOL1 (apolipoprotein L1)
EnsemblGeneIds (GRCh38): ENSG00000100342
EnsemblGeneIds (GRCh37): ENSG00000100342
OMIM: 603743, Gene2Phenotype
APOL1 is in 6 panels

2 reviews

Sophie Hambleton (Newcastle University)

Red List (low evidence)

Polymorphisms enriched in the African population are associated with increased protection from trypanosomiasis but also elevated risk of FSGS. Effect size is not that of a monogenic disorder
Created: 11 Jun 2018, 4:43 p.m.

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): APOL1 .PanelApp HGNC gene symbol check: APOL1 . IUIS Disease: Trypanosomiasis . IUIS Inheritance: AD .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: Somatic. IUIS Associated features: Trypanosomiasis. IUIS Major category: Defects in Intrinsic and Innate Immunity. IUIS Subcategory: Other Inborn Errors of Immunity Related to Non-Hematopoietic Tissues
Created: 2 Jul 2018, 10:35 a.m.
External expert review notes Red status due to no evident link to immunodeficiency, so I have kept this gene Red on this panel
Created: 12 Jun 2018, 3:30 p.m.
Comment on list classification: Changed status from Amber to Red. Only associated with susceptibility to Trypanosomiasis and not directly causative of it
Created: 11 May 2018, 11:25 a.m.
Only associated with susceptibility to Trypanosomiasis and not directly causative of it
Created: 11 May 2018, 11:25 a.m.
Comment on publications: Added publications to support APOL1 and susceptibility to Trypanosomiasis. Human African Trypanosomiasis, HAT (also known as sleeping sickness) manifests as an acute form caused by Trypanosoma brucei rhodesiense (Tbr) and a chronic form caused by Trypanosoma brucei gambiense (Tbg). Previous studies have suggested a host genetic role in infection outcomes, particularly for APOL1.
Studies in the Democratic Republic of Congo (DRC), Cameroon, Cote D’Ivoire, Guinea and Uganda have found evidence for polymorphisms in HP, IL6 and APOL1 associated with outcome of infection PMID: 16720107;28537557;15894515;28827791;29077717. PMID 29470556 (2018) findings differed from recent studies carried out in the Tbr HAT another endemic area of Uganda showed the APOL1 (Apolipoprotein 1) G2 allele to be protective against the disease which merits further investigation.
Created: 11 May 2018, 11:22 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: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: APOL-I, PanelApp HGNC gene symbol check: APOL1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Defects in innate immunity / Trypanosomias / Trypanosomias
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: APOL1, GRID_Gene_Symbol: APOL1, GRID_Transcript_ENS_Community submitted: ENST00000319136, GRID_Transcript_RefSeq: NM_145343.2, GRID_Transcript_ENS_used_on_Production: ENST00000319136
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • IUIS Classification December 2019
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • Expert Review Red
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Trypanosomias
  • Trypanosomiasis
  • Defects in Intrinsic and Innate Immunity
  • Trypanosomiasis, susceptibility to
OMIM
603743
Clinvar variants
Variants in APOL1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

28 Feb 2020, Gel status: 1

Added New Source, Set mode of inheritance, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to APOL1. Mode of inheritance for gene APOL1 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Added phenotypes Trypanosomiasis for gene: APOL1 Publications for gene APOL1 were updated from 25100047; 29470556; 16720107; 28537557; 15894515; 28827791; 29077717 to 28827791; 29470556; 32048120; 28537557; 16720107; 15894515; 25100047; 29077717; 32086639

12 Jul 2018, Gel status: 1

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: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene APOL1 were set to Trypanosomiasis, susceptibility to, Trypanosomias, Trypanosomiasis, Defects in Intrinsic and Innate Immunity

26 Jun 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to APOL1. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to APOL1. Panel: Primary immunodeficiency disorders

12 Jun 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: apol1 has been classified as Red List (Low Evidence).

11 May 2018, Gel status: 1

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

11 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for APOL1 were set to 25100047; 29470556; 16720107; 28537557; 15894515; 28827791; 29077717

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to APOL1. 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 APOL1. Panel: Primary immunodeficiency disorders Phenotypes for gene APOL1 were set to Trypanosomiasis, susceptibility to, Trypanosomias

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene APOL1 were set to Trypanosomiasis, susceptibility to

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

APOL1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

APOL1 was created by Louise Daugherty