Cytopenia - NOT Fanconi anaemia

Gene: SMARCAL1

Red List (low 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 17 panels

2 reviews

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

Gene reviewed due to Haematology Specialist Test Group considering the inclusion of relevant neutropenia thrombocytopenia genes. The Specialist Test Group 21st October 2019 (consisting of 4 centres: WWMGLH, NWGLH, YNEGLH, LSGLH) all agree to rate this gene Red on this panel. Additional comments from Haematology Specialist Test Group (Copy of Extra genes R91_consensus_v2.xlsx) 21st October 2019. Wessex and West Midlands GLH: Multisystem disorder, skeletal defects seem to be consistently present, has not been associated with a cytopenia as presenting symptom; North West GLH:Syndromic, not isolated thrombocytopenia; Yorkshire and North East GLH:no comment submitted; London South GLH: no comment submitted
Created: 4 Nov 2019, 7:30 p.m. | Last Modified: 4 Nov 2019, 7:30 p.m.
Panel Version: 0.135
Comment on list classification: As discussed with the GMS Haematology Specialist Test Group at workshop 2nd July 2019. Gene was not submitted by all GLHs so needed further review by all the GLHs. All agreed that this gene should be downgraded from Green to Red. Noted by YNEGLH as syndromic
Created: 22 Jul 2019, 2:55 p.m. | Last Modified: 22 Jul 2019, 2:55 p.m.
Panel Version: 0.116
Initial gene list (Consensus Genes for Haem Panels 17.12.18_KCH.xlsx) collated by Frances Smith Viapath Kings College Hospital February 2019 on behalf of London South GLH for the GMS Haematology specialist test group. Gene Symbol submitted: SMARCAL1; Suggested intial gene rating: Green List (high evidence); Are variants in this gene part of your current diagnostic practice? Yes; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Phenotypes: 242900 Schimke immunoosseous dysplasia; PMID(s): 17089404
Created: 8 Feb 2019, 1:43 p.m.

Frances Smith (King's College Hospital)

Green List (high evidence)

Gene rating submitted by Frances Smith Viapath Kings College Hospital February 2019 on behalf of London South GLH for the GMS Haematology specialist test group.
Created: 8 Feb 2019, 1:37 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
242900 Schimke immunoosseous dysplasia

Variants in this GENE are reported as part of current diagnostic practice

History Filter Activity

4 Nov 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source Expert review Red was added to SMARCAL1.

4 Nov 2019, Gel status: 1

Added New Source, Added New Source, Added New Source

Louise Daugherty (Genomics England Curator)

Source Wessex and West Midlands GLH was added to SMARCAL1. Source Yorkshire and North East GLH was added to SMARCAL1. Source North West GLH was added to SMARCAL1.

4 Nov 2019, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SMARCAL1 were changed from 242900 Schimke immunoosseous dysplasia to Schimke immunoosseous dysplasia, 242900

22 Jul 2019, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: smarcal1 has been classified as Red List (Low Evidence).

8 Feb 2019, Gel status: 3

Added New Source, Status Update

Louise Daugherty (Genomics England Curator)

Source Expert Review Green was added to SMARCAL1. Rating Changed from Red List (low evidence) to Green List (high evidence)

8 Feb 2019, Gel status: 1

Set mode of inheritance, Set Phenotypes

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene SMARCAL1 was changed from to BIALLELIC, autosomal or pseudoautosomal Added phenotypes 242900 Schimke immunoosseous dysplasia for gene: SMARCAL1

8 Feb 2019, Gel status: 1

Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Added phenotypes 242900 Schimke immunoosseous dysplasia for gene: SMARCAL1 Publications for gene SMARCAL1 were changed from to 17089404

8 Feb 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to SMARCAL1.

8 Feb 2019, Gel status: 1

Created, Added New Source, Set mode of inheritance

Louise Daugherty (Genomics England Curator)

gene: SMARCAL1 was added gene: SMARCAL1 was added to Cytopenia - NOT Fanconi anaemia. Sources: London South GLH Mode of inheritance for gene: SMARCAL1 was set to