Intellectual disability - microarray and sequencing
Gene: AP1S1 Green List (high evidence)Green List (high evidence)
Comment on phenotypes: extended phenotype description, added OMIM MIMidCreated: 17 Sep 2018, 10:11 a.m.
Comment on list classification: New gene added by external reviewer. Rated green based on external review comment, internal assessment (supportive functional data) and further publications to support gene-disease association.Created: 17 Sep 2018, 10:05 a.m.
New gene added by external expert review, who notes French Canadian (founder effect); however, Sephardic Jewish family also reported with a different variant. ID is part of the phenotype, added publication to support gene-disease association.
The patients cases described in the literature to date are likely to be linked to a founder effect. 5 children from 3 families all from Quebec, Canada (with the same mutation) and 1 patient from a consanguineous Sephardic-Jewish background has been described (a different mutation in AP1S1).
However, this gene was rated Green on the Vici Syndrome and other autophagy disorders panel for MEDNIK syndrome after discussion with Emma Baple (South West GMC and Genomics England); as there is a second, independent case with a different variant, plus functional data, so this gene can be green on the ID panel, since intellectual disability is part of the phenotypeCreated: 17 Sep 2018, 10:02 a.m.
Comment on publications: Additional publications to support upgrading of the gene to GreenCreated: 17 Sep 2018, 9:44 a.m.
Green List (high evidence)
Most reported families are French Canadian (founder effect); however, Sephardic Jewish family also reported with a different variant. ID is part of the phenotype. Merits at least Amber.Created: 22 Jun 2018, 10:15 a.m.
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
MEDNIK syndrome
Publications
Variants in this GENE are reported as part of current diagnostic practice
Source Victorian Clinical Genetics Services was added to AP1S1.
Phenotypes for gene: AP1S1 were changed from MEDNIK syndrome to MEDNIK syndrome, 609313; MEDNIK syndrome; mental retardation, enteropathy, deafness, peripheral neuropathy, ichthyosis and keratoderma syndrome
Gene: ap1s1 has been classified as Green List (High Evidence).
Publications for gene: AP1S1 were set to 23423674
AP1S1 was added to Intellectual disability panel. Sources: Literature
AP1S1 was created by Zornitza Stark
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.