Fetal anomalies
Gene: NEK9 Green List (high evidence)The rating of this gene has been updated following NHS Genomic Medicine Service approval.Created: 16 Mar 2022, 3:29 p.m. | Last Modified: 16 Mar 2022, 3:29 p.m.
Panel Version: 1.842
Comment on list classification: There is now sufficient evidence to promote this gene to Green at the next GMS panel update (added 'for-review' tag). At least 3 unrelated families presenting a similar fetally-relevant phenotype in association with different biallelic variants in this gene.
NEK9 is associated with relevant phenotypes in OMIM (MIM# 614262 and 617022) but currently is not in Gene2Phenotype.Created: 18 Jan 2021, 2:58 p.m. | Last Modified: 18 Jan 2021, 2:58 p.m.
Panel Version: 1.158
Green List (high evidence)
Deden et al (2020) report a further family with two consecutive prenatal presentations with compound heterozygous NEK9 variants. Both fetuses had arthrogryposis.
Both variants were reported as VUS when detected in the first fetus, which initially presented with 'short long bones, bowed femur, micrognathia, talipes and deviated hand' but re-evaluated after the phenotype progressed to arthrogryposis and then the next pregnancy showed the same ultrasound abnormalities and the same compound het variants. At this point the authors felt this represented a conclusive diagnosis.Created: 22 Oct 2020, 6:07 p.m. | Last Modified: 22 Oct 2020, 6:07 p.m.
Panel Version: 1.107
Shaheen et al 2016 reported 3 affected individuals in one consanguineous Saudi family with arthrogryposis apparent since early childhood, avascular necrosis of the hip (Perthes disease), and upward gaze palsy.
Casey et al 2016 reported 4 affected fetuses in two Irish Traveller families: phenotype = fetal akinesia, shortening of all long bones, multiple contractures, rib anomalies, thoracic dysplasia, pulmonary hypoplasia. The two families are thought to be distantly related to one another.
Therefore, this represents two affected families so probably not enough evidence for Green rating yet until more cases reported.Created: 6 Oct 2020, 3:38 p.m. | Last Modified: 6 Oct 2020, 3:38 p.m.
Panel Version: 1.98
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Arthrogryposis; short long bones
Publications
I don't know
DDG2P rating in original PAGE list: Probable.Created: 11 Dec 2018, 9:05 a.m.
Gene: nek9 has been classified as Green List (High Evidence).
Tag for-review was removed from gene: NEK9.
Gene: nek9 has been classified as Amber List (Moderate Evidence).
Publications for gene: NEK9 were set to 26908619
Tag for-review tag was added to gene: NEK9.
Phenotypes for gene: NEK9 were changed from Lethal congenital contracture syndrome 10 617022 to ?Arthrogryposis, Perthes disease, and upward gaze palsy, OMIM:614262; Arthrogryposis, Perthes disease, and upward gaze palsy, MONDO:0013660; Lethal congenital contracture syndrome 10, OMIM:617022; NEK9-related lethal skeletal dysplasia, MONDO:0014870
gene: NEK9 was added gene: NEK9 was added to Fetal anomalies. Sources: PAGE Additional Gene List,Expert Review Amber Mode of inheritance for gene: NEK9 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NEK9 were set to 26908619 Phenotypes for gene: NEK9 were set to Lethal congenital contracture syndrome 10 617022
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.