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Intellectual disability

Gene: SETD1B

Green List (high evidence)

SETD1B (SET domain containing 1B)
EnsemblGeneIds (GRCh38): ENSG00000139718
EnsemblGeneIds (GRCh37): ENSG00000139718
OMIM: 611055, Gene2Phenotype
SETD1B is in 4 panels

4 reviews

Ivone Leong (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Promoted from amber to green as there is now sufficient evidence to support a gene-disease association, based on submitted reviews.
Created: 24 Jun 2019, 10:11 a.m. | Last Modified: 24 Jun 2019, 10:11 a.m.
Panel Version: 2.880
A recent publication (PMID: 31110234) reported on a third case of a Japanese patient with a de novo frameshift variant in SETD1B with intellectual disability, developmental delay and myoclonic seizures. Previously, there were 2 unrelated cases of Japanese patients with de novo variants in this gene and 4 unrelated cases of patients with de novo 12q24.3 deletion encompassing SETD1B. All SNV variants are different.
Created: 24 Jun 2019, 10:06 a.m. | Last Modified: 24 Jun 2019, 10:06 a.m.
Panel Version: 2.878

Publications

Konstantinos Varvagiannis (Other)

I don't know

Apart from the patients by Hiraide et al. (PMID: 29322246) there seems to be no other relevant individual published, at least with clinical details.

In Decipher, patient 368813 has a de novo frameshift variant (p.Leu742ProfsTer100) which has been submitted as likely pathogenic, associated with delayed speech and language development, mild ID, ASD, and abnormal eating behavior and associated growth abnormality (overweight).

There are also 2 further individuals with DDD research variants in this gene and abnormality of the nervous system [1 missense, 1 frameshift - https://decipher.sanger.ac.uk/gene/SETD1B#variants/SETD1B/ddd-research-variant-overlap].

Additional patients with de novo variants and developmental disorder, ID, ASD appear in the denovo-db:
http://denovo-db.gs.washington.edu/denovo-db/QueryVariantServlet?searchBy=Gene&target=SETD1b

ClinVar has no relevant submissions (of SNVs).

SETD1B is not associated with any phenotype in OMIM, nor in G2P.

This gene is included in gene panels for ID offered by diagnostic laboratories (incl. Radboudumc).
Created: 20 Dec 2018, 9:28 a.m.

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

Louise Daugherty (Genomics England Curator)

I don't know

As a result of watchlist tag audit the watchlist tag was removed from SETD1B- this is now a green gene with sufficient evidence/review
Created: 13 Jan 2020, 4:11 p.m. | Last Modified: 13 Jan 2020, 4:11 p.m.
Panel Version: 3.0
added watchlist tag
Created: 27 Jul 2018, 3:31 p.m.
Comment on list classification: Rated gene as Amber based on current information in the literature, external expert review and internal clinical review
Created: 27 Jul 2018, 3:31 p.m.
After internal clinical review it as decided to leave this gene as rated Amber and not promote to Green, this is in view of the deletion cases being broader and containing several other genes. Recommend adding watch list tag.
Created: 27 Jul 2018, 3:29 p.m.
Past onto clinical team for further review and consideration of upgrading gene to Green. Hiraide T et al. (2018) PMID: 29322246 summarised the clinical features of SETD1B variants, including two unrelated cases reported in this publication that had missense de novo variants they also reviewed previous reports of four previously reported individuals with a de novo 12q24.3 deletion encompassing SETD1B (Baple et al. 2010; Labonne et al. 2016; Palumbo et al. 2015; Qiao et al. 2013). Study suggests that SETD1B aberration is likely to be the core defect in 12q24.3 deletion syndrome.
Created: 24 Jul 2018, 4:33 p.m.
Comment on publications: In addition to the publication describing denovo missense vars PMID:29322246, added publications describing microdeletions Labonne et al. (2016) PMID: 27106595 and Palumbo (2015) PMID: 25428890
Created: 24 Jul 2018, 3:42 p.m.
Comment on phenotypes: added phenotypes from publications
Created: 24 Jul 2018, 3:39 p.m.
Comment on list classification: New amber gene added by external expert review, who notes Two individuals from unrelated families with de novo variants , ID is part of the phenotype.
Created: 24 Jul 2018, 3:21 p.m.

Zornitza Stark (Australian Genomics)

I don't know

Two individuals from unrelated families with de novo variants in this gene reported in the literature. Consider inclusion as Amber in anticipation of further cases.
Created: 22 Jun 2018, 2:35 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Publications

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

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Victorian Clinical Genetics Services
Phenotypes
  • Epilepsy, developmental delay, intellectual disability, autistic behavior and craniofacial dysmorphic features
OMIM
611055
Clinvar variants
Variants in SETD1B
Penetrance
None
Publications
Panels with this gene

History Filter Activity

13 Jan 2020, Gel status: 3

Removed Tag

Louise Daugherty (Genomics England Curator)

Tag watchlist was removed from gene: SETD1B.

24 Jun 2019, Gel status: 3

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: setd1b has been classified as Green List (High Evidence).

24 Jun 2019, Gel status: 2

Set publications

Ivone Leong (Genomics England Curator)

Publications for gene: SETD1B were set to 29322246; 27106595; 25428890

29 Sep 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to SETD1B.

27 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: setd1b has been classified as Amber List (Moderate Evidence).

24 Jul 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SETD1B were set to Epilepsy, developmental delay, intellectual disability, autistic behavior and craniofacial dysmorphic features

24 Jul 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SETD1B were set to 29322246; 27106595; 25428890

24 Jul 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SETD1B were set to Intellectual disability, epilepsy, autism; epilepsy, developmental delay, intellectual disabilities, autistic behavior and craniofacial dysmorphic features

24 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: setd1b has been classified as Amber List (Moderate Evidence).

24 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: setd1b has been classified as Amber List (Moderate Evidence).

22 Jun 2018, Gel status: 0

Added New Source

Zornitza Stark (Australian Genomics)

SETD1B was added to Intellectual disability panel. Sources: Literature

22 Jun 2018, Gel status: 0

Created

Zornitza Stark (Australian Genomics)

SETD1B was created by Zornitza Stark