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Primary immunodeficiency

Gene: SMARCAL1

Green List (high evidence)

SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1)
EnsemblGeneIds (GRCh38): ENSG00000138375
EnsemblGeneIds (GRCh37): ENSG00000138375
OMIM: 606622, Gene2Phenotype
SMARCAL1 is in 16 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

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

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, 4:25 p.m. | Last Modified: 14 Oct 2020, 4:25 p.m.
Panel Version: 2.312
The following PubMed IDs were added to gene SMARCAL1 (OMIM gene MIM#606622): 17089404;11799392. These publications have been associated with the gene by the immunodeficiencies 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 list classification: Rating this gene green as >3 cases of likely disease causing variants.
Created: 16 May 2018, 10:49 a.m.
In OMIM this gene is associated with Schimke immunoosseous dysplasia. One of the diagnostic features of this disorder is T-cell immunodeficiency. OMIM reports that Boerkoel et al. (2002) (PMID: 11799392) determined that mutations in SMARCAL1 are responsible for SIOD. They looked at patients from 26 unrelated families and observed that affected individuals from 13 of 23 families with severe disease had 2 alleles with nonsense, frameshift, or splicing mutations, whereas affected individuals from 3 of 3 families with milder disease had a missense mutation on each allele. These observations indicated that some missense mutations allow retention of partial SMARCAL1 function and thus cause milder disease. Clewing et al. (2007)(PMID: 17089404) stated that 43 different mutations in the SMARCAL1 gene had been identified. They found that in 4 patients with a presumed monoallelic, heterozygous mutation in the SMARCAL1 gene, expressed RNA and/or protein from the other allele was not found, suggesting that in fact these 4 patients had biallelic SMARCAL1 mutations, though the second mutation was not found. Gene2Phenotype has a confirmed disease association between SMARCAL1 and Schimke immuno-osseous dysplasia. Rating this gene green as >3 cases of likely disease causing variants.
Created: 16 May 2018, 10:48 a.m.
Comment on phenotypes: Added MIM number to Schimke immunoosseous dysplasia
Created: 16 May 2018, 8:48 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

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): SMARCAL1 .PanelApp HGNC gene symbol check: SMARCAL1 . IUIS Disease: Schimke Immuno-osseous Dysplasia . IUIS Inheritance: AR .T cells: Low CD8, Nl CD4, absent MHC I on lymphocytes, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Short stature, spondiloepiphyseal dysplasia, intrauterine growth retardation, nephropathy, bacterial, viral, fungal infections, may present as SCID, bone marrow failure. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Immuno-osseous Dysplasias
Created: 2 Jul 2018, 10:35 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, 3:01 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: SMARCAL1, PanelApp HGNC gene symbol check: SMARCAL1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / Schimke disease / Schimke disease
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: SMARCAL1, GRID_Gene_Symbol: SMARCAL1, GRID_Transcript_ENS_Community submitted: ENST00000357276, GRID_Transcript_RefSeq: NM_014140.3, GRID_Transcript_ENS_used_on_Production: ENST00000357276
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
  • Schimke immunoosseous dysplasia 242900
  • Schimke disease
  • Short stature, spondiloepiphyseal dysplasia, intrauterine growth retardation, nephropathy, bacterial, viral, fungal infections, may present as SCID, bone marrow failure
  • Combined immunodeficiencies with associated or syndromic features
OMIM
606622
Clinvar variants
Variants in SMARCAL1
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: smarcal1 has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to SMARCAL1. 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 SMARCAL1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to SMARCAL1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SMARCAL1.

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 SMARCAL1 were set to Schimke immunoosseous dysplasia 242900, Schimke disease, Short stature, spondiloepiphyseal dysplasia, intrauterine growth retardation, nephropathy, bacterial, viral, fungal infections, may present as SCID, bone marrow failure, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to SMARCAL1. 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 SMARCAL1. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: smarcal1 has been classified as Green List (High Evidence).

13 Jun 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SMARCAL1 were set to 11799392; 17089404

16 May 2018, Gel status: 3

Gene classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

16 May 2018, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for SMARCAL1 were set to Schimke immunoosseous dysplasia 242900; Schimke disease

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).

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 SMARCAL1. Panel: Primary immunodeficiency disorders Phenotypes for gene SMARCAL1 were set to Schimke immunoosseous dysplasia, Schimke disease

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene SMARCAL1 were set to Schimke immunoosseous dysplasia

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

SMARCAL1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

SMARCAL1 was created by Louise Daugherty