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Intellectual disability

Gene: DLL1

Green List (high evidence)
DLL1 (delta like canonical Notch ligand 1)
EnsemblGeneIds (GRCh38): ENSG00000198719
EnsemblGeneIds (GRCh37): ENSG00000198719
OMIM: 606582, Gene2Phenotype
DLL1 is in 5 panels

4 reviews

Sarah Leigh (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 9 Mar 2022, 3:40 p.m. | Last Modified: 9 Mar 2022, 3:40 p.m.
Panel Version: 3.1510
Created: 9 Mar 2022, 3:40 p.m.
Last Modified: 9 Mar 2022, 3:40 p.m.
Panel version: 3.1510

Catherine Snow (Genomics England)

Green List (high evidence)

Comment on list classification: Comment on list classification: There is a sufficient number of cases to rate this gene Green at the next GMS panel update.
Created: 8 Oct 2020, 1:53 p.m. | Last Modified: 8 Oct 2020, 1:53 p.m.
Panel Version: 3.388
Sufficient number of unrelated individuals identified in PMID:31353024 with number of different variants for DLL1 to be associated with ID phenotype.
DLL1 also identified as a key gene in 6q27 deletions PMID: 31602192 and the most common phenotypes observed in the subset of patients analysed were developmental delay and/or learning difficulties observed in 86% of the patients (12/14)
DLL1 Is possible in G2P and reviewed in OMIM.
Created: 8 Oct 2020, 1:51 p.m. | Last Modified: 8 Oct 2020, 1:51 p.m.
Panel Version: 3.387

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

Phenotypes
Neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures 618709

Publications

Created: 8 Oct 2020, 1:51 p.m.
Last Modified: 8 Oct 2020, 1:51 p.m.
Panel version: 3.387

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Fifteen individuals from 12 unrelated families reported.
Created: 1 Feb 2020, 9:40 a.m. | Last Modified: 1 Feb 2020, 9:40 a.m.
Panel Version: 3.0

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Intellectual disability; autism; seizures; variable brain abnormalities; scoliosis

Publications

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

Created: 1 Feb 2020, 9:40 a.m.
Last Modified: 1 Feb 2020, 9:40 a.m.
Panel version: 3.0

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Heterozygous DLL1 pathogenic variants cause Neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures (# 618709).

Fischer-Zirnsak et al (2019 - PMID: 31353024) reported on 15 affected individuals from 12 unrelated families.

Most common features included DD/ID (12/14), ASD (6/14 - belonging to 6 families) or other behavioral abnormalities, seizures (6/14 - from 6 unrelated families) and various brain MRI abnromalities. As commented by OMIM (based on the same ref) "Cognitive function ranges from severely impaired to the ability to attend schools with special assistance". Among other features, scoliosis was observed in 4. The authors could not identify a distinctive facial gestalt.

Variable initial investigations (where discussed/performed - also suggesting relevance to the current panel) included CMA, FMR1, FLNA, mitochondrial DNA analysis and metabolic work-up but had not revealed an alternative cause.

The DLL1 variants were identified by WES (with the exception of a 122-kb microdeletion spanning DLL1 and FAM120B detected by CMA). Nonsense, frame-shift, splice-site variants in positions predicted to result to NMD were identified in most. One individual was found to harbor a missense variant (NM_005618.3:c.536G>T / p.Cys179Phe) and another the aforementioned microdeletion.

The variant in several individuals had occurred as a de novo event. In 2 families, it was inherited from an also affected parent (an unaffected sib was non-carrier) while in 3 families parental studies were not possible/complete.

In frame insertion of 4 residues was demonstrated for a splice site variant, from LCLs of the corresponding individual. For another individual, material was unavailable for mRNA studies. The missense variant affected a cysteine (of the DSL domain) conserved in all Notch ligands while AA changes affecting the same position of JAG1 (another Notch ligand) have been described in patients with Alagille s.

Based on the variants identified and reports of deletions spanning DLL1 in the literature, haploinsufficiency is the proposed underlying mechanism. The gene has also a pLI of 1 and %HI of 4.65.

DLL1 encodes the Delta-like canonical Notch ligand 1. Notch signaling is an established pathway for brain morphogenesis. Previous in vivo and in vitro studies have demonstrated the role of DLL1 in CNS. The gene is highly expressed in neuronal precursor cells during embryogenesis. Expression of Dll1 (and other molecules of the Notch signalling pathway) in an oscillatory/sustained pattern and cell-cell interactions important for this pathway have been demonstrated to play a role in neuronal differentiation. [Most discussed by Fischer-Zirnsak et al with several refs provided / also Gray et al., 1999 - PMID: 10079256 & OMIM].

Animal models as summarized by the authors:
[Mouse] Loss of Dll1 in mice has been shown to increase neuronal differentiation, cause CNS hyperplasia and increased number of neurons (PMIDs cited: 9109488, 12397111, 20081190). Reduced Dll1 expression was associated with scoliosis and mild vertebral defects (cited PMIDs: 19562077, 14960495, 22484060 / among others Dll1 haploinsufficiency and dominant negative models studied). Scoliosis and vertebral segmentation defects were features in 4 and 1 individual, respectively in the cohort of 15.
[Zebrafish] Homozygous mutations in dlA, the zebrafish ortholog, disrupted the Delta-Notch signaling and led to patterning defects in the hindbrain and overproduction of neurons (cited: 15366005).

Please consider inclusion in other possibly relevant panels e.g. for ASD.
Sources: Literature
Created: 29 Dec 2019, 12:17 p.m.

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

Phenotypes
Global developmental delay; Intellectual disability; Morphological abnormality of the central nervous system; Seizures; Behavioral abnormality; Autism; Scoliosis

Publications

Created: 29 Dec 2019, 12:17 p.m.

Panel version: 3.0

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
Phenotypes
  • Neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures, OMIM:618709
OMIM
606582
Clinvar variants
Variants in DLL1
Penetrance
unknown
Publications
Panels with this gene

History Filter Activity

10 Mar 2022, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review was removed from gene: DLL1.

9 Mar 2022, Gel status: 3

Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to DLL1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

27 Jul 2021, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: DLL1 were changed from Global developmental delay; Intellectual disability; Morphological abnormality of the central nervous system; Seizures; Behavioral abnormality; Autism; Scoliosis to Neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures, OMIM:618709

8 Oct 2020, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: DLL1 were set to 31353024

8 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Catherine Snow (Genomics England)

Gene: dll1 has been classified as Amber List (Moderate Evidence).

8 Oct 2020, Gel status: 0

Added Tag

Catherine Snow (Genomics England)

Tag for-review tag was added to gene: DLL1.

29 Dec 2019, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: DLL1 was added gene: DLL1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: DLL1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: DLL1 were set to 31353024 Phenotypes for gene: DLL1 were set to Global developmental delay; Intellectual disability; Morphological abnormality of the central nervous system; Seizures; Behavioral abnormality; Autism; Scoliosis Penetrance for gene: DLL1 were set to unknown Review for gene: DLL1 was set to GREEN