Intellectual disability - microarray and sequencing
Gene: SCYL1 Green List (high evidence)Green List (high evidence)
The rating of this gene has been updated following NHS Genomic Medicine Service approval.Created: 14 Mar 2022, 2:22 p.m. | Last Modified: 14 Mar 2022, 2:22 p.m.
Panel Version: 3.1519
Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. At least six variants reported in five cases of OMIM:616719 with mild to severe intellectual disability (PMID: 26581903, 29419818, 30531813). Together with supportive functional and animal data (PMID: 17571074, 26581903)Created: 26 May 2021, 11:42 a.m. | Last Modified: 26 May 2021, 11:42 a.m.
Panel Version: 3.1097
Comment on list classification: Gene identified in literature PMID:30914295 as missing in PanelApp compared to other curated gene list for ID genes.
Schmidt et al (PMID: 26581903) reported on two families with three individuals affected by a previously unsubscribed ataxia syndrome. Siblings, born to unrelated healthy parents of white European descent with British and German roots and an individual born to non-consanguineous parents with at least three generations of Cuban family history.
Both affected siblings were found to harbour two mutations within SCYL1 (SCY1-like, kinase-like [MIM: 607982]), c.937delG (p.Val313Cysfs*6) in exon 7 and c.1509_1510delTG (p.Ala504Profs*15) in exon 11 (GenBank: NM_020680.3. One sib had normal cognition; the other had mild intellectual disability.
The other unrelated individual was reported to have SCYL1 variant with a splice-site mutation (c.1230+1G>A [p.?]) affecting the invariable +1 nucleotide of intron 9 (causing disruption of correct mRNA splicing by inducing skipping of exon 9, which encodes part of the HEAT repeat domain) and a premature termination mutation (c.1636C>T [p. Gln546*]) in exon 12.They were also reported to have mild learning disability.
SCYL1 is probable in Gene2Phenotype but no phenotypes assigned to the entry. SCYL1 in OMIM as Spinocerebellar ataxia, autosomal recessive 21.
As only two unrelated cases have been identified and ID has been classed as mild and not in all individuals, SCYL1 will be classified as Amber and added to the watchlist.Created: 30 May 2019, 3:02 p.m.
Tag Q2_21_rating was removed from gene: SCYL1.
Source Expert Review Green was added to SCYL1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Tag watchlist was removed from gene: SCYL1. Tag Q2_21_rating tag was added to gene: SCYL1.
Publications for gene: SCYL1 were set to 26581903; 30914295
Phenotypes for gene: SCYL1 were changed from Spinocerebellar ataxia, autosomal recessive 21, 616719 to Spinocerebellar ataxia, autosomal recessive 21 OMIM:616719; acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome MONDO:0014744
Tag watchlist tag was added to gene: SCYL1.
Mode of inheritance for gene SCYL1 was changed from to BIALLELIC, autosomal or pseudoautosomal
gene: SCYL1 was added gene: SCYL1 was added to Intellectual disability. Sources: Literature,Expert Review Amber Mode of inheritance for gene: SCYL1 was set to Publications for gene: SCYL1 were set to 26581903; 30914295 Phenotypes for gene: SCYL1 were set to Spinocerebellar ataxia, autosomal recessive 21, 616719
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.