Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism

Abstract

ANKRD17 is an ankyrin repeat-containing protein thought to play a role in cell cycle progression, whose ortholog in Drosophila functions in the Hippo pathway as a co-factor of Yorkie. Here, we delineate a neurodevelopmental disorder caused by de novo heterozygous ANKRD17 variants. The mutational spectrum of this cohort of 34 individuals from 32 families is highly suggestive of haploinsufficiency as the underlying mechanism of disease, with 21 truncating or essential splice site variants, 9 missense variants, 1 in-frame insertion-deletion, and 1 microdeletion (1.16 Mb). Consequently, our data indicate that loss of ANKRD17 is likely the main cause of phenotypes previously associated with large multi-gene chromosomal aberrations of the 4q13.3 region. Protein modeling suggests that most of the missense variants disrupt the stability of the ankyrin repeats through alteration of core structural residues. The major phenotypic characteristic of our cohort is a variable degree of developmental delay/intellectual disability, particularly affecting speech, while additional features include growth failure, feeding difficulties, non-specific MRI abnormalities, epilepsy and/or abnormal EEG, predisposition to recurrent infections (mostly bacterial), ophthalmological abnormalities, gait/balance disturbance, and joint hypermobility. Moreover, many individuals shared similar dysmorphic facial features. Analysis of single-cell RNA-seq data from the developing human telencephalon indicated ANKRD17 expression at multiple stages of neurogenesis, adding further evidence to the assertion that damaging ANKRD17 variants cause a neurodevelopmental disorder.

Keywords: ANKRD17; Hippo pathway; Mask; Yorkie; ankyrin repeats; dysmorphism; intellectual disability; neurodevelopmental syndrome; speech delay.

Figure 1

Distribution of pathogenic ANKRD17 variants and 4q13.3 deletions (A) Variants affecting coding sequence. Truncating variants are in red. Domain boundaries are based on Uniprot entry O75179. AR, ankyrin repeats; KH, K Homology domain. (B) Variants affecting essential splice sites. Exon-intron structure drawn approximately to scale (apart from intron 1), according to GenBank: NM_032217.4. (C) Deletions of the region containing ANKRD17 on chromosome 4q13.3. Among the disease-associated OMIM genes in the interval (those in green), the mode of inheritance or associated phenotype is not compatible with that of the deletions shown. Only deletions under 5 Mb from the DECIPHER database are shown. For DECIPHER individuals 349955 and 271532, publicly available clinical information is listed; individual 321792 is one of three affected individuals of the previously described familial case (the phenotypes listed on the figure are a summary of all three family members); and individual 355915 corresponds to individual 6 in the present report (see Table S1 for details). ID, intellectual disability; GD, growth delay; CV, cardiovascular; abns, abnormalities; SNHL, sensorineural hearing loss.

Figure 2

Dysmorphic facial features of the ANKRD17-related disorder Physical characteristics include a triangular face (I1, 4, 5, 6, 9, 15, 22, 30, 31, and 33), high anterior hairline (I1-10, 12, 15, 18, 25, 29, 30, 31, 32, and 33), deep set (I2, 3, 6, 7, 30) or almond-shaped (I1, 4, 5, 12, 15, 22, 29, and 33) eyes with periorbital fullness (I1, 3, 4, 5, 8, 12), full cheeks (I2, 6, 7, 12, 18, 26, and 29), thick alae nasi with flared nostrils (I2, 3, 5, 6, 8, 9, 12, 25, 31), and a thin upper lip (I1, 3, 4, 5, 9, 10, 11, 15, 22, 26, 30, and 31).

Figure 3

Conservation of amino acids affected by ANKRD17 non-truncating variants, across ankyrin repeats Alignment of the 25 ankyrin repeats of human ANKRD17. The repeats, as defined by UniProtKB, were downloaded and aligned in UCSF Chimera. Amino acids affected by non-truncating variants are boxed in red. In the Consensus row, amino acids in red are 100% identical. Beneath the alignment, the numbering refers to the 30-amino acid repeating sequence of each ankyrin repeat, and the predicted positions of structural motifs that define ankyrin repeats are depicted (note that sequence corresponding to the canonical C-terminal beta-turn was not included in the UniProtKB-defined ANKRD17 ankyrin repeats).

Figure 4

Predicted three-dimensional structure of ANKRD17 ankyrin repeats and amino acids affected by missense variants (A) Ankyrin repeats 16–25 of human ANKRD17 (GenBank: NP_115593) were modeled using the SWISS-MODEL homology-modeling server and visualized in UCSF Chimera. For each repeat, alpha-helix 1 is in orange and alpha-helix 2 is in blue. (B) Detail of ANKRD17 ankyrin repeat 23, showing the positions of the invariant leucines (magenta) and glycine (cyan), which are altered at the equivalent positions in other repeats of ANKRD17 (indicated in brackets). Superscripts for Leu⁶, Gly¹³, and Leu²¹ refer to numbering within the 30-amino acid repeating sequence presented in Figure 3. Thin yellow lines indicate predicted hydrogen bonds.

Figure 5

Single-cell RNA-seq analysis of ANKRD17, ANKHD1, YAP1, and CDK2 expression in the developing human telencephalon Single-cell RNA-seq data were visualized at the UCSC Cell Browser (dataset: Cortex development). The dataset was generated from 4,261 cells obtained from the telencephalon (cortex and/or ganglionic eminences) of 48 fetuses, ranging in age from 6 to 37 post-conception weeks (pcw) (with the majority of cells from 9–16.5 pcw samples). Data are plotted using the “t-SNE on WGCNA” layout. Upper left panel indicates clusters of cell types in detail (see https://cells.ucsc.edu/?ds=cortex-dev for definitions). In the gene panels, the degree of brown shading in each cell represents transcript abundance, light blue shading indicates absence of detected expression, and broad categories of cell types of interest are outlined in red. MGE, medial ganglionic eminence.