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Primary immunodeficiency

Gene: HPS6

Green List (high evidence)

HPS6 (HPS6, biogenesis of lysosomal organelles complex 2 subunit 3)
EnsemblGeneIds (GRCh38): ENSG00000166189
EnsemblGeneIds (GRCh37): ENSG00000166189
OMIM: 607522, Gene2Phenotype
HPS6 is in 9 panels

4 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)

Red List (low evidence)

Louise Daugherty (Genomics England Curator)

I don't know

Hermansky-Pudlak - OCA, bleeding, lysosomal ceroid storage: green association, phenotype
Created: 26 Sep 2019, 3:55 p.m. | Last Modified: 26 Sep 2019, 3:55 p.m.
Panel Version: 1.130
Comment on list classification: Changed rating from Red to Green. There is strong evidence for gene:disease association, the query previously for this gene was the phenotype, however The Immunology Specialist Test Group during webex call 28th March 2019 recommended Green rating, the phenotype was relevant to the panel for GMS, and further confirmed in follow up email on 20th June (North West GLH) and 6th September (London North GLH).
Created: 17 Sep 2019, 5:10 p.m. | Last Modified: 17 Sep 2019, 5:10 p.m.
Panel Version: 1.99
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
Comment on list classification: Red status due to no evident link to immunodeficiency, so I have kept this gene Red on this panel until further evidence.
Created: 19 Jun 2018, 4:03 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.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • North West GLH
  • London North GLH
  • GOSH PID v.8.0
Phenotypes
  • Hermansky-Pudlak syndrome 6, 614075
OMIM
607522
Clinvar variants
Variants in HPS6
Penetrance
None
Panels with this gene

History Filter Activity

17 Sep 2019, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: HPS6 were changed from Hermansky-Pudlak syndrome 6 to Hermansky-Pudlak syndrome 6, 614075

17 Sep 2019, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: hps6 has been classified as Green List (High Evidence).

17 Sep 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to HPS6.

17 Sep 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to HPS6.

17 Sep 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to HPS6.

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.

6 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: hps6 has been classified as Red List (Low Evidence).

19 Jun 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: hps6 has been classified as Red List (Low Evidence).

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to HPS6. Panel: Primary immunodeficiency disorders

6 Apr 2018, Gel status: 1

Clear Sources

Louise Daugherty (Genomics England Curator)

HPS6 Source: GOSH PID 20171155 was removed from gene: HPS6

6 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID v.8.0 was added to HPS6. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

HPS6 was added to Primary immunodeficiency disorders panel. Sources: GOSH PID 20171155

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

HPS6 was created by Louise Daugherty