Intellectual disability
Gene: DPF2 Green List (high evidence)Green List (high evidence)
Comment on list classification: Changed from Red to Green, there is now enough evidence to support the intellectual disability phenotypeCreated: 9 Aug 2018, 8:17 a.m.
Comment on publications: Added publication suggested from external expert review to support upgrading of the gene to GreenCreated: 9 Aug 2018, 8:15 a.m.
Comment on mode of pathogenicity from expert review. Appears to be dominant negative effects from missense mutations rather than LOF. ref: Vasileiou et al., (2018) PMID: 29429572 "Despite the intolerance to loss-of function variants (as evidenced by the high pLI value), haploinsufficiency seems unlikely given that the annotation of deletions encomprassing DPF2 in normal populations indicates that a complete loss of one allele could be neutral. On the contrary,the clustering of all variants within an evolutionarily highly concerved region, as previously described for other BAF subunits (SMARCA4, SMARCA2, SMARCB1, and SMARCE1), the nuclear aggregation phenotype, and the recruitment of wild-type DPF2 and BRG1 to the aggregates indicate a dominant negative effect.Created: 9 Aug 2018, 8:14 a.m.
added dominant-negative tagCreated: 9 Aug 2018, 8:12 a.m.
Comment on mode of inheritance: added MO suggested by expert review and publicationCreated: 9 Aug 2018, 8:11 a.m.
New review added by external expert who notes that there are now 8 unrelated individuals reported by Vasileiou et al., (2018) PMID: 29429572 with features of Coffin-Siris syndrome, ID is part of the phenotype. The publication supports gene-disease association and rating of this gene to Green.Created: 9 Aug 2018, 8:06 a.m.
Green List (high evidence)
PMID: 29429572 reports DPF2 as a new Coffin-Siris gene. The protein interacts with other subunits of the BAF complex.
They reported de novo mutations in DPF2 [OMIM: 601671], "encoding a subunit of the BAF chromatin-remodelling complex, which has not previously been associated with neurodevelopmental syndromes. In total, we identified eight unrelated individuals (four females and four males) with features of Coffin-Siris syndrome"
Functional and computational evidence was also provided to support pathogenicity:
"In summary, the following lines of evidence support the pathogenicity of the identified DPF2 variants: (1) their de novo occurrence, (2) the PHD finger mutational hotspot, (3) the intolerance of DPF2 and especially its encoded tandem PHD finger domain to variation, and (4) the fact that functional analyses of the missense alterations showed abolished or attenuated H3 binding and the formation of nuclear DPF2 aggregates."
Appears to be dominant negative effects from missense mutations rather than LOF
"Despite the intolerance to loss-of function variants (as evidenced by the high pLI value),
haploinsufficiency seems unlikely given that the annotation of deletions encomprassing DPF2 in normal populations indicates that a complete loss of one allele could be neutral. On the contrary,the clustering of all variants within an evolutionarily highly concerved region, as previously described for other BAF subunits (SMARCA4, SMARCA2, SMARCB1, and SMARCE1), the nuclear aggregation phenotype, and the recruitment of wild-type DPF2 and BRG1 to the aggregates indicate a dominant negative effect."Created: 8 Aug 2018, 1:43 p.m.
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
Coffin-Siris syndrome 7 618027
Publications
Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Red List (low evidence)
Red List (low evidence)
Not related to a disease in OMIM or Gene2Phenotype. Not evidence found related to clinical ID cases in literature search. Candidate gene for ID in PMID 26350204.Created: 27 Oct 2017, 2:46 p.m.
Publications
Red List (low evidence)
Gene: dpf2 has been classified as Green List (High Evidence).
Phenotypes for gene: DPF2 were set to Coffin-Siris syndrome 7, 618027; intellectual disability
Publications for gene: DPF2 were set to 26350204; 29429572
Mode of pathogenicity for gene: DPF2 was changed to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Mode of inheritance for gene: DPF2 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Mode of inheritance for gene: DPF2 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Mode of inheritance for gene: DPF2 was changed from to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
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.
Publications for gene DPF2 was set to ['26350204']
The Gel status was updated for this whole panel
The Gel status was updated for this whole panel
DPF2 was added to Intellectual disabilitypanel. Sources: Expert Review Red
DPF2 was created by ellenmcdonagh
If promoting or demoting a gene, please provide comments to justify a decision to move it.
Genes included in a Genomics England gene panel for a rare disease category (green list) should fit the criteria A-E outlined below.
These guidelines were developed as a combination of the ClinGen DEFINITIVE evidence for a causal role of the gene in the disease(a), and the Developmental Disorder Genotype-Phenotype (DDG2P) CONFIRMED DD Gene evidence level(b) (please see the original references provided below for full details). These help provide a guideline for expert reviewers when assessing whether a gene should be on the green or the red list of a panel.
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.
AND
D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic setting(iv).
AND
E. No convincing evidence exists or has emerged that contradicts the role of the gene in the specified phenotype.
(i)Plausible disease-causing mutations: Recurrent de novo mutations convincingly affecting gene function. Rare, fully-penetrant mutations - relevant genotype never, or very rarely, seen in controls. (ii) Interpretable functional region: ORF in protein coding genes miRNA stem or loop. (iii) Phenotype: the rare disease category, as described in the eligibility statement. (iv) Intermediate penetrance genes should not be included.
It’s assumed that loss-of-function variants in this gene can cause the disease/phenotype unless an exception to this rule is known. We would like to collect information regarding exceptions. An example exception is the PCSK9 gene, where loss-of-function variants are not relevant for a hypercholesterolemia phenotype as they are associated with increased LDL-cholesterol uptake via LDLR (PMID: 25911073).
If a curated set of known-pathogenic variants is available for this gene-phenotype, please contact us at [email protected]
We classify loss-of-function variants as those with the following Sequence Ontology (SO) terms:
Term descriptions can be found on the PanelApp homepage and Ensembl.
If you are submitting this evaluation on behalf of a clinical laboratory please indicate whether you report variants in this gene as part of your current diagnostic practice by checking the box
Standardised terms were used to represent the gene-disease mode of inheritance, and were mapped to commonly used terms from the different sources. Below each of the terms is described, along with the equivalent commonly-used terms.
A variant on one allele of this gene can cause the disease, and imprinting has not been implicated.
A variant on the paternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on the maternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on one allele of this gene can cause the disease. This is the default used for autosomal dominant mode of inheritance where no knowledge of the imprinting status of the gene required to cause the disease is known. Mapped to the following commonly used terms from different sources: autosomal dominant, dominant, AD, DOMINANT.
A variant on both alleles of this gene is required to cause the disease. Mapped to the following commonly used terms from different sources: autosomal recessive, recessive, AR, RECESSIVE.
The disease can be caused by a variant on one or both alleles of this gene. Mapped to the following commonly used terms from different sources: autosomal recessive or autosomal dominant, recessive or dominant, AR/AD, AD/AR, DOMINANT/RECESSIVE, RECESSIVE/DOMINANT.
A variant on one allele of this gene can cause the disease, however a variant on both alleles of this gene can result in a more severe form of the disease/phenotype.
A variant in this gene can cause the disease in males as they have one X-chromosome allele, whereas a variant on both X-chromosome alleles is required to cause the disease in females. Mapped to the following commonly used term from different sources: X-linked recessive.
A variant in this gene can cause the disease in males as they have one X-chromosome allele. A variant on one allele of this gene may also cause the disease in females, though the disease/phenotype may be less severe and may have a later-onset than is seen in males. X-linked inactivation and mosaicism in different tissues complicate whether a female presents with the disease, and can change over their lifetime. This term is the default setting used for X-linked genes, where it is not known definitately whether females require a variant on each allele of this gene in order to be affected. Mapped to the following commonly used terms from different sources: X-linked dominant, x-linked, X-LINKED, X-linked.
The gene is in the mitochondrial genome and variants within this can cause this disease, maternally inherited. Mapped to the following commonly used term from different sources: Mitochondrial.
Mapped to the following commonly used terms from different sources: Unknown, NA, information not provided.
For example, if the mode of inheritance is digenic, please indicate this in the comments and which other gene is involved.