SFARI Gene release notes for Q1 2018

April 17, 2018

*Notes prepared by Eric Larsen, Marcel Estevez, Ishita Das, Anjali Sarkar, Girish Nagendra, Ravi Kollu, and Sharmila Banerjee-Basu of MindSpec, Inc., and edited by Alan Packer of SFARI.

Human Gene module

A total of 17 new genes were added to the Human Gene module, bringing the total number to
1,007. In depth annotation of 522 rare variants and 39 common variants was also completed, and
112 new references were added. Noteworthy genes added include:

Gene Scoring module

A total of 118 gene scores were added, including 17 newly annotated genes. Additionally, nine previously scored genes were moved to a higher category based on recent publications. Another set of 11 genes were updated with new evidence but did not merit a higher score. Genes with updated scores include ATP1A3CHD2, FRMPD4, MED13L, MTOR, PHIP, SLC6A1, TSC2, and TTN.

Copy Number Variant (CNV) module

A total of 7 newly curated references and 17 novel CNV loci were added to the CNV module, resulting in a total of 563 curated references and 2,242 CNV loci.

Animal Models module

The mouse model dataset was updated with 29 new models, including Ahrgef10, Ambra1, Dagla, Dlgap1, Kirrel3, Otud7a, Slc9a9, and Taok2. Additionally, many mouse models based on high-confidence genes were added, including Cacna1c, Met, and Shank3. Eleven new rescue models were also added.

Mouse model annotation highlights include:

Ambra1 heterozygous mutant mice show female specific deficits in social interaction, decreased ultrasound communication in adults and pups, increased tendency for repetitive behaviors, and reduced cognitive flexibility. Sexual dimorphism of the Ambra1 heterozygous phenotype is partly explained by a strong reduction in Ambra1 protein in the cerebral cortex of females but not males (Dere et al., 2014).
See Ambra1

Slc9a9-deficient mice exhibit impaired social interaction, repetitive behaviors, and altered sensory processing. In addition, they show hyperacidic endosomes, a cell-autonomous defect in glutamate receptor expression, and impaired neurotransmitter release due to a defect in presynaptic calcium entry (Ullman et al., 2018).
See Slc9a9

Kirrel3-null mice display preference for a mouse over a non-social object but not significant preference for a stranger mouse over a familiar mouse. These mice also show impaired ultrasonic communications, increased locomotor activity and repetitive rearing, as well as enhanced performance on the rotarod and hypersensitivity to acoustic stimuli.
See Kirrel3

The rat model dataset has been updated with 17 new models and new data for 4 existing models. The dataset includes 7 new ASD models from existing environmental inducers (isolation, poly I:C, and valproic acid).

Rat model annotation highlights include:

Shank3 knockout rats were tested in a novel radial maze test with a pro-social USV playback. All rats were responsive; however, Shank3 null male rats showed decreased exploration of the proximal arm to the playback, once the playback stopped. This novel method of quantifying social approach produced a different result than the traditional three-chamber sociability test, where the same rets exhibited normal sociability (Berg et al., 2018).
See Shank3

A Pcdh19 knockdown model shows that this gene is important for pyramidal neuron lamination in the hippocampus, and for maintaining dendritic length for these neurons. Overexpressing human PCDH19 alongside the knockdown restores all associated phenotypes. Furthermore knockdown of Pcdh19, which is linked to female epilepsy, results in higher susceptibility to chemically-induced seizures (Bassani et al., 2018).
See Pcdh19

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SFARI Gene Update

We are pleased to announce some changes to the ongoing curation of the data in SFARI Gene. In the context of a continued effort to develop the human gene module and its manually curated list of autism risk genes, we are modifying other aspects of the site to focus on the information that is of greatest interest to the research community. The version of SFARI Gene that has been developed until now will be frozen and will remain available as “SFARI Gene Archive”. Please see the announcement for more details.
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