Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome
Authors: Cousin Margot A. , Veale Emma L. , Dsouza Nikita R. , Tripathi Swarnendu , Holden Robyn G. , Arelin Maria , Beek Geoffrey , Bekheirnia Mir Reza , Beygo Jasmin , Bhambhani Vikas , Bialer Martin , Bigoni Stefania , Boelman Cyrus , Carmichael Jenny , Courtin Thomas , Cogne Benjamin , Dabaj Ivana , Doummar Diane , Fazilleau Laura , Ferlini Alessandra , Gavrilova Ralitza H. , Graham John M. , Haack Tobias B. , Juusola Jane , Kant Sarina G. , Kayani Saima , Keren Boris , Ketteler Petra , Klöckner Chiara , Koopmann Tamara T. , Kruisselbrink Teresa M. , Kuechler Alma , Lambert Laëtitia , Latypova Xénia , Lebel Robert Roger , Leduc Magalie S. , Leonardi Emanuela , Lewis Andrea M. , Liew Wendy , Machol Keren , Mardini Samir , McWalter Kirsty , Mignot Cyril , McLaughlin Julie , Murgia Alessandra , Narayanan Vinodh , Nava Caroline , Neuser Sonja , Nizon Mathilde , Ognibene Davide , Park Joohyun , Platzer Konrad , Poirsier Céline , Radtke Maximilian , Ramsey Keri , Runke Cassandra K. , Guillen Sacoto Maria J. , Scaglia Fernando , Shinawi Marwan , Spranger Stephanie , Tan Ee Shien , Taylor John , Trentesaux Anne-Sophie , Vairo Filippo , Willaert Rebecca , Zadeh Neda , Urrutia Raul , Babovic-Vuksanovic Dusica , Zimmermann Michael T. , Mathie Alistair , Klee Eric W. 
Published: June 2022

Background

Genomics enables individualized diagnosis and treatment, but large challenges remain to functionally interpret rare variants. To date, only one causative variant has been described for KCNK9 imprinting syndrome (KIS). The genotypic and phenotypic spectrum of KIS has yet to be described and the precise mechanism of disease fully understood.

Methods

This study discovers mechanisms underlying KCNK9 imprinting syndrome (KIS) by describing 15 novel KCNK9 alterations from 47 KIS-affected individuals. We use clinical genetics and computer-assisted facial phenotyping to describe the phenotypic spectrum of KIS. We then interrogate the functional effects of the variants in the encoded TASK3 channel using sequence-based analysis, 3D molecular mechanic and dynamic protein modeling, and in vitro electrophysiological and functional methodologies.

Results

We describe the broader genetic and phenotypic variability for KIS in a cohort of individuals identifying an additional mutational hotspot at p.Arg131 and demonstrating the common features of this neurodevelopmental disorder to include motor and speech delay, intellectual disability, early feeding difficulties, muscular hypotonia, behavioral abnormalities, and dysmorphic features. The computational protein modeling and in vitro electrophysiological studies discover variability of the impact of KCNK9 variants on TASK3 channel function identifying variants causing gain and others causing loss of conductance. The most consistent functional impact of KCNK9 genetic variants, however, was altered channel regulation.

Conclusions

This study extends our understanding of KIS mechanisms demonstrating its complex etiology including gain and loss of channel function and consistent loss of channel regulation. These data are rapidly applicable to diagnostic strategies, as KIS is not identifiable from clinical features alone and thus should be molecularly diagnosed. Furthermore, our data suggests unique therapeutic strategies may be needed to address the specific functional consequences of KCNK9 variation on channel function and regulation.