FB2025_02 , released April 17, 2025
Human Disease Model Report: chromosome 16p11.2 deletion syndrome, 593-kb
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General Information
Name
chromosome 16p11.2 deletion syndrome, 593-kb
FlyBase ID
FBhh0001068
Disease Ontology Term
Parent Disease
Overview

The 16p11.2 deletion is a recurrent CNV (copy-number variant) extending approximately 593kb, a region that includes 25 unique genes. It is associated with a range of neurodevelopmental features, including autism, intellectual disability, epilepsy, and obesity. The variability of associated phenotypes and other findings suggest that the observed phenotypes in 16p11.2 deletion are not caused by haploinsufficiency of a single causative gene, but rather are caused by multiple dosage-sensitive genes in the region, which may also interact with each other.

Of the 25 human genes within the 16p11.2 deletion, fly orthologs of 14 were identified. Using RNAi-effected knockdown targeted at each fly gene, multiple cellular and neurodevelopmental phenotypes were assessed. Those with significant neurodevelopmental phenotypes include rl (orthologous to MAPK3; see FBhh0000842), Pp4-19C (orthologous to PPP4C), CG10465 (orthologous to KCTD13), Ald1 (orthologous to ALDOA), Tao (orthologous to TAOK2; see FBhh0001219), and Rph (orthologous to DOC2A). Phenotypes of pairwise knockdowns were assessed in the developing eye; interactions with other neurodevelopmental genes were also assessed in the developing eye. In a separate study, neurodevelopmental phenotypes at the larval neuromuscular junction are described for two fly kinesin genes, Klp68D and Klp64D; KIF22, one of many kinesin genes in human, is within the 16p11.2 deletion.

Results support a complex interaction model for disease pathogenicity, where multiple 16p11.2 genes are sensitive to dosage imbalance and participate in complex interactions; they both enhance and suppress the phenotypic effects of each other; they are also modulated by other genes in the genetic background.

[updated Apr. 2021 by FlyBase; FBrf0222196]

Disease Summary Information
Disease Summary: chromosome 16p11.2 deletion syndrome, 593-kb
OMIM report

[CHROMOSOME 16p11.2 DELETION SYNDROME, 593-KB](https://omim.org/entry/611913)

Human gene(s) implicated

[CHROMOSOME 16p11.2 DELETION SYNDROME, 593-KB](https://omim.org/entry/611913)

Symptoms and phenotype

The 16p11.2 recurrent microdeletion phenotype is characterized by developmental delay, intellectual disability, and/or autism spectrum disorder. Seizures are observed in approximately 20% of individuals; macrocephaly, seizures, and/or obesity are also observed in some individuals. [Gene Reviews, 16p11.2 Recurrent Microdeletion; 2019.06.28]

Chromosome 16p11.2 deletion syndrome is associated with a range of neurodevelopmental features, including autism and severe early-onset obesity. [from MIM:611913; 2019.06.28]

Genetics

Both microdeletions and microduplications can result from recurrent CNVs (copy-number variants). Recurrent CNVs generally arise by nonallelic homologous recombination during meiosis, with breakpoints in the large duplicated blocks of sequence flanking the CNV event. Because the breakpoints cluster within defined regions, the extent of recurrent CNVs is essentially identical even in unrelated individuals (Watson et al., 2014; pubmed:24773319).

Cellular phenotype and pathology
Molecular information
External links
Disease synonyms
chromosome 16p11.2 deletion syndrome
chromosome 16p11.2 deletion syndrome, 593kb
Ortholog Information
Human gene(s) in FlyBase
Other mammalian ortholog(s) used
    D. melanogaster Gene Information (6)
    Gene Snapshot
    rolled (rl) encodes the mitogen activated protein (MAP) kinase, core component of the RAS/MAPK pathway. It is inactivated by the phosphatases encoded by PTP-ER and Mkp3. It phosphorylates a diverse set of downstream cytoplasmic and nuclear effectors, which impact cell fate decisions in a wide array of tissues. [Date last reviewed: 2019-03-14]
    Gene Groups / Pathways
    Comments on ortholog(s)

    High-scoring ortholog of human MAPK1 and MAPK3 (1 Drosophila to 2 human). Dmel\rl shares 76-82% identity and 84-90% similarity with the human genes.

    Orthologs and Alignments from DRSC
    DIOPT - DRSC Integrative Ortholog Prediction Tool - Click the link below to search for orthologs in Humans
    Gene Groups / Pathways
    Comments on ortholog(s)

    High-scoring ortholog of human PPP4C (1 Drosophila to 1 human); multiple other homologous genes in both species. Dmel\Pp4-19C shares 91% identity and 96% similarity with the human gene.

    Orthologs and Alignments from DRSC
    DIOPT - DRSC Integrative Ortholog Prediction Tool - Click the link below to search for orthologs in Humans
    Molecular function (GO)
      Cellular component (GO)
        Gene Groups / Pathways
          Comments on ortholog(s)

          High-scoring ortholog of human KCTD10, KCTD13, TNFAIP1 (1 Drosophila to 3 human). Dmel\CG10465 shares 57-68% identity and 71-79% similarity with the human genes.

          Orthologs and Alignments from DRSC
          DIOPT - DRSC Integrative Ortholog Prediction Tool - Click the link below to search for orthologs in Humans
          Gene Snapshot
          Aldolase (Aldo) encodes an enzyme that catalyzes the reversible conversion of beta-D-fructose 1,6-bisphosphate into dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate, and thus plays an essential role in glycolysis and gluconeogenesis. It also catalyzes the conversion of beta-D-fructose 1-phosphate into dihydroxyacetone phosphate and D-glyceraldehyde and plays a role in fructose catabolism. [Date last reviewed: 2025-03-27]
          Cellular component (GO)
          Gene Groups / Pathways
          Comments on ortholog(s)

          High-scoring ortholog of human ALDOA, ALDOB, ALDOC (2 Drosophila to 3 human); the paralogous Drosphila gene is Ald2. Dmel\Ald1 shares 63-68% identity and 74-79% similarity with the human genes.

          Orthologs and Alignments from DRSC
          DIOPT - DRSC Integrative Ortholog Prediction Tool - Click the link below to search for orthologs in Humans
          Gene Snapshot
          Tao (Tao) encodes a Ser/Thr kinase belonging to the Mst/Ste20 family. It is implicated in the Hippo and PAR-1 pathways. It contributes to restriction of tissue growth during development, regulation of microtubule dynamics, neuronal polarity, neural development, ethanol-stimulated behavioral response, and apoptosis. [Date last reviewed: 2019-03-14]
          Gene Groups / Pathways
          Comments on ortholog(s)

          High-scoring ortholog of human TAOK1, TAOK2, TAOK3 (1 Drosophila to 3 human). Dmel\Tao shares 47-49% identity and 60-64% similarity with the human genes.

          Orthologs and Alignments from DRSC
          DIOPT - DRSC Integrative Ortholog Prediction Tool - Click the link below to search for orthologs in Humans
          Gene Groups / Pathways
          Comments on ortholog(s)

          Moderate- to high-scoring ortholog of RPH3A, DOC2B, DOC2A RPH3AL (1 Drosophila to 4 human). Dmel\Rph aligns only to RPH3A along the full length of the encoded protein. Rph shares 31-39% identity and 46-58% similarity with the human genes.

          Orthologs and Alignments from DRSC
          DIOPT - DRSC Integrative Ortholog Prediction Tool - Click the link below to search for orthologs in Humans
          Other Genes Used: Viral, Bacterial, Synthetic (0)
            Summary of Physical Interactions (129 groups)
            protein-protein
            Interacting group
            Assay
            References
            enzymatic study, autoradiography, pull down
            anti tag coimmunoprecipitation, anti tag western blot, peptide massfingerprinting
            anti tag coimmunoprecipitation, peptide massfingerprinting
            two hybrid, comigration in non denaturing gel electrophoresis, western blot, anti tag coimmunoprecipitation, pull down, autoradiography, anti tag western blot, cross-linking study, Identification by mass spectrometry
            anti bait coimmunoprecipitation, western blot, pull down, autoradiography, anti tag coimmunoprecipitation, anti tag western blot
            anti tag coimmunoprecipitation, western blot, proximity ligation assay, fluorescence microscopy
            anti tag coimmunoprecipitation, peptide massfingerprinting
            anti tag coimmunoprecipitation, peptide massfingerprinting
            anti tag coimmunoprecipitation, peptide massfingerprinting
            anti tag coimmunoprecipitation, anti tag western blot
            enzymatic study, autoradiography
            enzymatic study, autoradiography
            anti tag coimmunoprecipitation, anti tag western blot, western blot
            anti tag coimmunoprecipitation, anti tag western blot, pull down, autoradiography
            anti tag coimmunoprecipitation, anti tag western blot
            anti tag coimmunoprecipitation, peptide massfingerprinting
            anti bait coimmunoprecipitation, western blot
            enzymatic study, autoradiography
            anti tag coimmunoprecipitation, anti tag western blot
            anti tag coimmunoprecipitation, anti tag western blot
            anti tag coimmunoprecipitation, anti tag western blot
            anti tag coimmunoprecipitation, peptide massfingerprinting
            anti tag coimmunoprecipitation, peptide massfingerprinting
            pull down, autoradiography, anti tag coimmunoprecipitation, western blot
            RNA-protein
            Interacting group
            Assay
            References
            rna three hybrid
            protein-protein
            Interacting group
            Assay
            References
            anti tag coimmunoprecipitation, peptide massfingerprinting, anti tag western blot, pull down, western blot
            experimental knowledge based
            pull down, anti tag western blot, anti tag coimmunoprecipitation
            anti tag coimmunoprecipitation, western blot, peptide massfingerprinting
            anti tag coimmunoprecipitation, anti tag western blot
            anti tag coimmunoprecipitation, anti tag western blot
            anti tag coimmunoprecipitation, western blot, experimental knowledge based
            anti bait coimmunoprecipitation, western blot
            anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
            anti tag coimmunoprecipitation, anti tag western blot, pull down
            experimental knowledge based, anti tag coimmunoprecipitation, anti tag western blot
            RNA-protein
            Interacting group
            Assay
            References
            anti tag coimmunoprecipitation, partial DNA sequence identification by hybridization, anti bait coimmunoprecipitation
            protein-protein
            Interacting group
            Assay
            References
            RNA-protein
            Interacting group
            Assay
            References
            anti tag coimmunoprecipitation, quantitative reverse transcription pcr
            protein-protein
            Interacting group
            Assay
            References
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            anti tag coimmunoprecipitation, peptide massfingerprinting
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            anti bait coimmunoprecipitation, western blot, pull down, molecular weight estimation by staining, Identification by mass spectrometry
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            experimental knowledge based
            protein-protein
            Interacting group
            Assay
            References
            enzymatic study, western blot, anti tag coimmunoprecipitation, anti tag western blot
            protein kinase assay, anti tag western blot
            enzymatic study, western blot, anti tag coimmunoprecipitation, anti tag western blot
            Alleles Reported to Model Human Disease (Disease Ontology) (34 alleles)
            Models Based on Experimental Evidence ( 8 )
            Modifiers Based on Experimental Evidence ( 12 )
            Allele
            Disease
            Interaction
            References
            Models Based on Experimental Evidence ( 1 )
            Modifiers Based on Experimental Evidence ( 2 )
            Allele
            Disease
            Interaction
            References
            Models Based on Experimental Evidence ( 1 )
            Allele
            Disease
            Evidence
            References
            Modifiers Based on Experimental Evidence ( 1 )
            Allele
            Disease
            Interaction
            References
            Models Based on Experimental Evidence ( 1 )
            Allele
            Disease
            Evidence
            References
            Modifiers Based on Experimental Evidence ( 1 )
            Allele
            Disease
            Interaction
            References
            Models Based on Experimental Evidence ( 7 )
            Modifiers Based on Experimental Evidence ( 4 )
            Models Based on Experimental Evidence ( 3 )
            Modifiers Based on Experimental Evidence ( 2 )
            Allele
            Disease
            Interaction
            References
            Alleles Representing Disease-Implicated Variants
            Genetic Tools, Stocks and Reagents
            Sources of Stocks
            Contact lab of origin for a reagent not available from a public stock center.
            Bloomington Stock Center Disease Page
            Related mammalian, viral, bacterial, or synthetic transgenes
            Allele
            Transgene
            Publicly Available Stocks
            Selected Drosophila transgenes
            Allele
            Transgene
            Publicly Available Stocks
            RNAi constructs available
            Allele
            Transgene
            Publicly Available Stocks
            Selected Drosophila classical alleles
            Allele
            Allele class
            Mutagen
            Publicly Available Stocks
            P-element activity
            loss of function allele
            ethyl methanesulfonate
            amorphic allele - genetic evidence
            ethyl methanesulfonate
            loss of function allele
            amorphic allele - genetic evidence
            ethyl methanesulfonate
            amorphic allele - genetic evidence
            ethyl methanesulfonate
            loss of function allele
            loss of function allele
            spontaneous
            amorphic allele - genetic evidence
            ethyl methanesulfonate
            amorphic allele - genetic evidence
            ethyl methanesulfonate
            amorphic allele - genetic evidence
            X ray
            ethyl methanesulfonate
            amorphic allele - genetic evidence
            X ray
            loss of function allele
            ethyl methanesulfonate
            References (9)