Glossary

To help our users better understand the data contained within SFARI Gene, we have created a glossary defining some of the most common terms found throughout the database. The glossary will help contextualize information for users as they explore the website.

Animal Model

An animal model is an experimental organism—typically mouse, rat, zebrafish, or fruit fly—that carries a mutation or variant reported in an individual with autism. Characterization of animal models provides crucial insight into the underlying mechanisms of autism risk. SFARI Gene curates data from genetic, CNV, rescue, induced, and inbred animal models.

Associated Disorders

When disorders have been associated with an ASD candidate gene in the scientific literature, they are listed on the gene’s entry in the Human Gene module. Examples of disorders frequently identified in SFARI Gene include: bipolar disorder, epilepsy, schizophrenia, and developmental delay.

Associated Syndromes

When syndromes have been associated with an ASD candidate gene in the scientific literature, they are listed on the gene’s entry in the Human Gene module. Examples of such syndromes include: Phelan-McDermid syndrome, fragile X syndrome, Rett syndrome, and tuberous sclerosis.

Case

A case is an individual in which a particular variant has been observed and recorded. In the SFARI Gene database, this term is typically associated with individuals carrying copy number variants. Information on the individual cases in the CNV module can be found under the Individuals tab on any CNV entry.

CNV Model

CNV models are studies on animals in which a specific CNV has been generated. In SFARI Gene, CNV animal models can be viewed by selecting the CNV filtering button. Related single-gene genetic models as well as associated human CNVs curated in SFARI Gene are listed in the tabs of every CNV model entry.

CNV Scrubber

The CNV Scrubber shows the number of CNVs found at a particular locus, the number of reports curated, and whether a CNV is primarily caused by deletion or duplication.

Cohort

A cohort is a group of individuals (also known as a population) in which one or more variants have been identified. In the SFARI Gene database, this term is typically associated with cohorts screened for a particular copy number variant. Information on populations curated in SFARI Gene can be found under the Populations tab on any CNV entry.

Common Variants

Common variants are more frequently observed, typically occurring in more than 1% of individuals. The number of observed common variants in a particular gene can be found in every entry in the Human Gene module.

Deletion - Duplication

SFARI Gene records the type of genetic mutations that cause CNVs: deletion, duplication, or both. On the CNV Scrubber, when both deletion and duplication have been implicated as a cause of a CNV, a color gradient is used to indicate which is the more common cause.

De Novo

Variants that arise “de novo” occur in the sperm or egg cells of individuals who do not themselves carry the variant. The inheritance pattern of a variant can be found in its entry in either the Human Gene or CNV modules.

Gene Score

A gene score is a numeric or alphanumeric value calculated by SFARI Gene that is assigned to a gene to indicate the strength of the evidence linking it to ASD.

Genetic Model

Genetic animal models are studies on animals selected because of the existence of a mutation in a particular gene. In SFARI Gene, genetic animal models can be viewed by selecting the Genetic filtering button. Related rescue and CNV models are listed in the tabs on every genetic model entry.

Human Gene

The Human Gene module serves as a comprehensive, up-to-date reference for all known human genes associated with autism spectrum disorders (ASD).

Human Genome Scrubber

The Human Genome Scrubber maps ASD candidate genes by their location along the human genome and provides users with information including the assigned gene score and the number of reports associated with the gene.

Inbred Model

In the context of SFARI Gene, inbred models are ones that exhibit a particular phenotype of interest without carrying a known genetic mutation. Inbred animal models can be viewed by selecting the Inbred filtering button. Related rescue models are listed in the tabs on every inbred model entry.

Induced Model

Induced models are studies on animals in which a particular trait or disorder has been purposefully induced with a biological or chemical agent. In SFARI Gene, induced animal models can be viewed by selecting the Induced filtering button. The model name and the inducing factor’s name and subtype (chemical or biological) can be found in the main tables under the Induced page. Related rescue models can be found on individual induced model entries.

Inheritance Pattern

Some single-gene mutations and CNVs are inherited while others instead arise “de novo,” occurring in the sperm or egg cells of individuals who do not themselves carry the variant. The inheritance pattern is listed on entries in both the Human Gene and CNV modules.

Interactome

SFARI Gene’s interactome is a visual reference of the many protein interactions that occur between various gene products. This interactive feature also lets users click through to any interconnected genes that have also been curated in the database.

MindSpec

MindSpec is an independent, non-profit research organization that oversees the curation of data into SFARI Gene.

Model Genotype

The listed model genotype indicates whether the model described in the report carries one copy of the mutation (heterozygous) or two copies (homozygous).

Model Type

SFARI Gene catalogues many different animal model types, including genetic, rescue, inbred, CNV, and induced models.

Parent Profile

The parent profile is the description of an animal model before the study began. For example, the parent profile of a induced model would describe the animal subjects before the inducing factor was introduced.

Phenotype

In every entry in the Animal Model module, recorded phenotypes are listed to describe the characteristics of each animal carrying a mutation in a gene or CNV.

Protein Interaction

SFARI Gene catalogues protein interactions that occur between the gene products of known ASD candidate genes. There are six types of protein interactions in SFARI Gene: protein binding, promoter binding, RNA binding, protein modification, direct regulation, and autoregulation.

Rare Variants

Rare variants occur in only a small percentage of individuals, typically less than 1%. The number of observed rare variants in a particular gene can be found in every entry in the Human Gene module.

Rescue Model

Rescue animal models are studies on animals that have received either pharmaceutical, genetic, or cell transplant treatments during the course of the study. These treatments have the effect of ameliorating one or more of the associated phenotypes. In SFARI Gene, rescue animal models can be viewed by selecting the Rescue filtering button. The rescue model’s parent profile can be found in the tabs on every entry.

Ring Browser

SFARI Gene’s Ring Browser visualizes all the human genetic information contained in the database, including all known protein interactions.

Syndromic

Genes that are assigned the “Syndromic” distinction contain mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis.

Syntenic

Synteny refers to the preserved co-localization of a block of genes in chromosomes from different species. In SFARI Gene, entries for syntenic genes contain links to the relevant animal models.

Validated

For CNVs identified in individual cases, SFARI Gene catalogs whether or not the identified CNV has been independently validated. Those that have not are referred to as “unvalidated.” Validation status and method can be found under the Individuals tab on a CNV entry.