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Intellectual disability

Gene: SMARCA2

Green List (high evidence)

SMARCA2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2)
EnsemblGeneIds (GRCh38): ENSG00000080503
EnsemblGeneIds (GRCh37): ENSG00000080503
OMIM: 600014, Gene2Phenotype
SMARCA2 is in 6 panels

6 reviews

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Please also note that Cappuccio et al (2020 - PMID: 32694869) report on individuals with de novo SMARCA2 variants with features of a novel, blepharophimosis-intellectual disability syndrome (BIS) but whose clinical presentation did not fit a diagnosis of Nicolaides-Baraitser (NB) syndrome.

Clinical details on 14 subjects with BIS were provided, DD/ID being a universal feature (14/14 - moderate to severe ID). Compared to other syndromes with blepharophimosis, lack of ptosis (observed in only 14% in this cohort), epicanthus inversus and limb abnormalities were proposed to distinguish BIS from other recognizable syndromes with blepharophimosis.

All individuals with BIS were found to harbor de novo missense variants. These clustered outside the helicase domain and localized within exons 8,9 and 19.

Few (6) additional individuals with de novo missense variants (in ex. 8, 14, 19) did not fit either diagnosis (NB or BIS) with the SNVs classified as VUS.

According to Cappuccio et al, most individuals with diagnosis of NB syndrome harbor variants spanning exons 15 to 25 [corresponding to the ATPase domain, which in turn is split in a Helicase ATP-Binding domain (720-912) and a helicase C-terminal domain (1080-1164)]. Most NB-associated variants are missense and rarely in-frame exon deletions.

As also commented on CNVs (deletions or duplications) encompassing SMARCA2 have been reported in individuals with DD/ID although these did not fit a diagnosis of NB syndrome (and CNVs were rather not intragenic/limited to SMARCA2) [cited PMIDs: 31530938, 28846756].

Transcriptomic and methylation signatures confirmed molecular stratification of affected individuals with SMARCA2-related disorders (and controls).
Created: 26 Jul 2020, 10:34 a.m. | Last Modified: 26 Jul 2020, 10:34 a.m.
Panel Version: 3.201

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

Caroline Wright (Sanger)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
COFFIN SIRIS

Publications

  • 0

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_gilissen_2014_known;in_UKGTN_v12 . Main mutation mechanism : All missense/in frame; Loss of function
Created: 27 Jul 2017, 8:29 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; find_uk10k; gilissen_2014_known; UKGTN_v12; Nijmegen_ID_diagnostic; Nijmegen_ID_candidates; GEL_ID_green_20160217; neuro_20160418_strict; All missense/in frame; Loss of function. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 1:24 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

Mode of pathogenicity

Alice Gardham (Genomics England)

Comment when marking as ready: Causes a small number of cases of Coffin Siris. Recognised on G2P
Created: 23 Nov 2016, 9:33 a.m.

alisdair mcneill (Sheffield childrens hospital)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
intellectual disability; coffin-siris syndrome

Publications

  • http://www.ncbi.nlm.nih.gov/pubmed/25169878

Lu Raymond (university of cambridge )

Green List (high evidence)

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Nicolaides-Baraitser syndrome, 601358
  • COFFIN SIRIS
OMIM
600014
Clinvar variants
Variants in SMARCA2
Penetrance
Complete
Panels with this gene

History Filter Activity

29 Sep 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to SMARCA2.

12 Mar 2018, Gel status: 3

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 1

Set Mode of Inheritance, Added New Source

Ellen McDonagh (Genomics England Curator)

SMARCA2 was added to Intellectual disabilitypanel. Source: Expert Review Green Model of inheritance for gene SMARCA2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

SMARCA2 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen