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22q11.2 recurrent (DGS/VCFS) region (proximal, A-B) (includes TBX1) Loss
ISCA-37433-Loss 3
22q11.2 recurrent (DGS/VCFS) region (proximal, A-D) (includes TBX1) Loss
ISCA-37446-Loss 2

Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: MYSM1

MYSM1 (Myb like, SWIRM and MPN domains 1)
EnsemblGeneIds (GRCh38): ENSG00000162601
EnsemblGeneIds (GRCh37): ENSG00000162601
OMIM: 612176, Gene2Phenotype
MYSM1 is in 5 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, 1:34 p.m. | Last Modified: 14 Oct 2020, 1:34 p.m.

Panel Version: 2.282

The following PubMed IDs were added to gene MYSM1 (OMIM gene MIM#612176): 24288411;28115216;22184403. 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

Publications

Created: 13 Oct 2020, 9:36 a.m.
Last Modified: 13 Oct 2020, 9:36 a.m.
Panel version: 2.208

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

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

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)

4 cases in 3 kindreds plus mouse model
Created: 11 Jun 2018, 1:21 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Bone marrow failure; neurodevelopmental delay; mid-face hypoplasia; immunodeficiency

Publications

Created: 11 Jun 2018, 1:21 p.m.

Panel version: 0.821

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): MYSM1 .PanelApp HGNC gene symbol check: MYSM1 . IUIS Disease: MYSM1 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Immature B cells, .IUIS Other affected cells: N/A. IUIS Associated features: Short stature, recurrent infections, congenital bone marrow failure, myelodysplasia, immunodeficiency affecting B-cells and granulocytes, skeletal anomalies, cataracts, developmental delay.. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Immuno-osseous Dysplasias
Created: 2 Jul 2018, 10:35 a.m.

Comment on list classification: Changed Red to Green from external review comment and further publications to support gene-disease association
Created: 13 Jun 2018, 9:45 a.m.

Comment on publications: added mouse model publication 28446309; 22184403
Created: 13 Jun 2018, 9:34 a.m.

Comment on phenotypes: Added phenotypes suggested from external expert review.
Created: 13 Jun 2018, 9:28 a.m.

Comment on mode of inheritance: Added MOI from external expert review
Created: 13 Jun 2018, 9:27 a.m.

Comment on publications: Added publications suggested from external expert review to support upgrading of the gene to Green
Created: 13 Jun 2018, 9:26 a.m.

Comment on mode of inheritance: Added MOI from external expert review
Created: 13 Jun 2018, 9:26 a.m.

Original metadata downloaded from ESID Registry. ESID_Gene_original: MYSM1, PanelApp HGNC gene symbol check: MYSM1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / MYSM1 deficiency / MYSM1 deficiency
Created: 17 Apr 2018, 12:29 p.m.

Created: 17 Apr 2018, 12:29 p.m.

Panel version: 1.94

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
ESID Registry 20171117

Phenotypes

MYSM1 deficiency
Bone marrow failure
neurodevelopmental delay
mid-face hypoplasia
immunodeficiency
Short stature, recurrent infections, congenital bone marrow failure, myelodysplasia, immunodeficiency affecting B-cells and granulocytes, skeletal anomalies, cataracts, developmental delay.
Combined immunodeficiencies with associated or syndromic features

OMIM

612176

Clinvar variants

Variants in MYSM1

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: mysm1 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 MYSM1. Publications for gene MYSM1 were updated from 24288411; 26220525; 28115216; 28446309; 22184403; 26474655 to 26474655; 26220525; 24288411; 28446309; 28115216; 22184403 Rating Changed from Green List (high evidence) to Red List (low evidence)

17 Sep 2019, Gel status: 3