Intellectual disability - microarray and sequencing
Gene: TLK2 Green List (high evidence)Comment on list classification: New evidence to promote this gene from Red to Green has arisen. A publication (Reijnders & Miller et al, AJHG, published online May 31, 2018) reports heterozygous loss-of-function or missense variants in this gene in 38 unrelated individuals and two affected mothers. Affected individuals had mild-boderline neurodevelopmental delay, behavioral disorders, severe gastro-intestinal problems and facial dysmorphism. 6% of the individuals had normal IQ levels (85–100), 14% had borderline ID (IQ
70–85), and from the 72% diagnosed with ID (IQ < 70), most had mild ID (IQ 50–70). 3 individuals were too young for formal assessment of their neurodevelopmental phenotype, but all had language and motor delay. Five loss-of-function variants were identified in gnomAD at a frequency of around 0.00002. None of the missense were identified in Exac or an in-house database of healthy individuals. Only one missense variant was identified in gnomAD in one individual (an allele frequency of 0.000004). The pseudogenes similar to TLK2 were investigated, and the sequences at the site of each recurrent mutation corresponded to wild-type TLK2, excluding a gene conversion mechanism. Analysis of ExAC demonstrated TLK2 is extremely intolerant for LOF variants with a pLI score of 1. Tlk2-null mice have been previously reported as embryonically lethal, due to placental failure.Created: 1 Jun 2018, 7:33 a.m.
Comment on mode of inheritance: Heterozygous de novo or maternally inherited variants reported in Reijnders & Miller et al, AJHG (2018).Created: 1 Jun 2018, 7:08 a.m.
Comment on publications: New publication "De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder" Reijnders & Miller et al, AJHG, published Online: May 31, 2018. (https://doi.org/10.1016/j.ajhg.2018.04.014 - PMID not yet available).Created: 1 Jun 2018, 7:07 a.m.
Red List (low evidence)
Added gene to panel but insufficient evidence to rate as diagnostic-grade. Current evidence comes from PMID:27479843 (2016) who perform meta-analysis on 2,637 de novo mutations identified from the exomes of 2,104 patient-parent trios, and identify TLK2 as a candidate ID gene.Created: 31 Oct 2017, 10:18 a.m.
Phenotypes
intellectual disability
Publications
Publications for gene: TLK2 were set to 27479843; https://doi.org/10.1016/j.ajhg.2018.04.014
Phenotypes for gene: TLK2 were changed from intellectual disability to Mental retardation, autosomal dominant 57, OMIM:618050; Mental retardation, autosomal dominant 57, MONDO:0054837
Source Victorian Clinical Genetics Services was added to TLK2.
Gene: tlk2 has been classified as Green List (High Evidence).
Mode of inheritance for gene: TLK2 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TLK2 were set to 27479843; https://doi.org/10.1016/j.ajhg.2018.04.014
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.
TLK2 was added to Intellectual disability panel. Sources: Expert Review Red
TLK2 was created by Ellen McDonagh
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.