DDG2P
Gene: TRAF7 Green List (high evidence)Green List (high evidence)
The 'watchlist' tag was removed as there is only one gene-disease association currently present in the DD panel in G2P database (July 2023) and the rating for this panel is strong (equivalent to green in PanelApp).Created: 7 Oct 2023, 8:21 a.m. | Last Modified: 7 Oct 2023, 8:22 a.m.
Panel Version: 3.61
The DDG2P confidence category for the disease Developmental Delay Congenital Anomalies and Dysmorphic Features is strong. The allelic requirement and mutation consequence are monoallelic_autosomal and altered gene product structure (PMID:29961569).Created: 4 Oct 2023, 5:08 p.m. | Last Modified: 4 Oct 2023, 5:08 p.m.
Panel Version: 3.12
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes
Developmental Delay Congenital Anomalies and Dysmorphic Features
Publications
Mode of pathogenicity
Other
Green List (high evidence)
Kept 'watchlist' tag when adding in new DD-G2P gene-disorder from March 2019; although DDG2P has multiple ratings (probable and confirmed), the three disorders are very similar (Developmental Delay Congenital Anomalies and Dysmorphic Features, Developmental Delay, Congenital Anomalies, and Dysmorphic Features, Developmental delay, congenital malformations and dysmorphism).Created: 19 Apr 2019, 3:40 p.m.
New gene:disorder association added to DDG2P in March 2019: Developmental Delay Congenital Anomalies and Dysmorphic Features. DDG2P Disease confidence: probable. DDG2P mode of pathogenicity/mutation consequence: all missense/in frame. DDG2P mode of inheritance: monoallelic.Created: 19 Apr 2019, 3:34 p.m.
Multiple DD-Gene2Phenotype ratings (confirmed; probable). Changed rating to Green to reflect highest DD-G2P Disease confidence: confirmed for Developmental Delay, Congenital Anomalies, and Dysmorphic Features.Created: 28 Jan 2019, 2:29 p.m.
Added watchlist tag to highlight different DD-G2P ratings for different gene:disorder associations.Created: 19 Nov 2018, 4:54 p.m.
DDG2P rating for Developmental delay, congenital malformations and dysmorphism: probable. DDG2P Mode of inheritance: monoallelic. DDG2P mode of pathogenicity: all missense/in frame.
DDG2P rating for Developmental Delay, Congenital Anomalies, and Dysmorphic Features: confirmed. DDG2P Mode of inheritance: monoallelic. DDG2P mode of pathogenicity: all missense/in frame.
Created: 19 Nov 2018, 11:31 a.m.
Phenotypes for gene: TRAF7 were changed from Developmental Delay Congenital Anomalies and Dysmorphic Features to Developmental Delay Congenital Anomalies and Dysmorphic Features
Tag watchlist was removed from gene: TRAF7.
Phenotypes for gene: TRAF7 were changed from Developmental Delay Congenital Anomalies and Dysmorphic Features to Developmental Delay Congenital Anomalies and Dysmorphic Features
Phenotypes for gene: TRAF7 were changed from Developmental Delay, Congenital Anomalies, and Dysmorphic Features; Developmental delay, congenital malformations and dysmorphism to Developmental Delay Congenital Anomalies and Dysmorphic Features
Mode of pathogenicity for gene TRAF7 was changed from Other - please provide details in the comments to Other
Publications for gene: TRAF7 were set to 29961569
Rebecca Foulger: DDG2P mode of pathogenicity fo
Gene: traf7 has been classified as Green List (High Evidence).
Tag watchlist tag was added to gene: TRAF7.
Added phenotypes Developmental Delay, Congenital Anomalies, and Dysmorphic Features for gene: TRAF7
gene: TRAF7 was added gene: TRAF7 was added to DDG2P. Sources: Expert Review Amber,DD-Gene2Phenotype Mode of inheritance for gene: TRAF7 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: TRAF7 were set to 29961569 Phenotypes for gene: TRAF7 were set to Developmental delay, congenital malformations and dysmorphism Mode of pathogenicity for gene: TRAF7 was set to Other - please provide details in the comments
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.