Human Gene Module / Chromosome X / CDK16

CDK16cyclin dependent kinase 16

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
2 / 3
Rare Variants / Common Variants
4 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
Xp11.3
Associated Disorders
-
Relevance to Autism

A de novo nonsense variant in the CDK16 gene was identified in a male ASD proband from the Autism Sequencing Consortium in Satterstrom et al., 2020. A maternally-inherited frameshift variant in the CDK16 gene had previously been found to segregate with intellectual disability and spasticity in four males from an extended multiplex family in Hu et al., 2016; Leitao et al., 2022 subsequently reported that affected males in this family also presented with ASD and absence seizures. Leitao et al., 2022 also identified two previously unreported individuals with CDK16 variants: a 42-year-old male patient with intellectual disability and spasticity with a CDK16 nonsense variant; and a male patient with ASD, intellectual disability, and epilepsy from a family whose history was compatible with X-linked inheritance with a potentially deleterious missense variant.

Molecular Function

The protein encoded by this gene belongs to the cdc2/cdkx subfamily of the ser/thr family of protein kinases. It may play a role in signal transduction cascades in terminally differentiated cells; in exocytosis; and in transport of secretory cargo from the endoplasmic reticulum. This gene is thought to escape X inactivation.

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Reports related to CDK16 (3 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes Hu H et al. (2016) No ASD, epilepsy/seizures
2 Primary Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
3 Recent Recommendation - Leito E et al. (2022) Yes Epilepsy/seizures
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.46C>T p.Arg16Ter stop_gained De novo - - 31981491 Satterstrom FK et al. (2020)
c.961G>T p.Glu321Ter stop_gained Unknown - Simplex 36323681 Leito E et al. (2022)
c.1039G>T p.Gly347Cys missense_variant Familial Maternal Extended multiplex 36323681 Leito E et al. (2022)
c.976_977del p.Asp326Ter frameshift_variant Familial Maternal Extended multiplex 25644381 Hu H et al. (2016)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

Score Delta: Score remained at 2

criteria met
See SFARI Gene'scoring criteria
2

Strong Candidate

See all Category 2 Genes

We considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.

1/1/2023
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2

Increased from to 2

Krishnan Probability Score

Score 0.56893310524162

Ranking 1078/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
Original Source
ExAC Score

Score 0.99570261568942

Ranking 1471/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Original Source
Sanders TADA Score

Score 0.93298862667218

Ranking 12138/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Original Source
Zhang D Score

Score -0.34743512603168

Ranking 17802/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
Original Source
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