Four subtypes of disease-causing missense mutations underlie pathogenic protein interactions in neurodegenerative VPS13A disease
Xing Lin, Yuta Ryoden, Chigure Suzuki, Hiroyuki Ishikawa, Takaharu Sakuragi, Yasuo Uchiyama, Shigekazu Nagata
Xing Lin, Yuta Ryoden, Chigure Suzuki, Hiroyuki Ishikawa, Takaharu Sakuragi, Yasuo Uchiyama, Shigekazu Nagata
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Research Article Genetics Neuroscience

Four subtypes of disease-causing missense mutations underlie pathogenic protein interactions in neurodegenerative VPS13A disease

Abstract

VPS13A is an intracellular lipid transfer protein comprising more than 3,000 amino acids. Mutations in human VPS13A cause VPS13A disease, a neurodegenerative disorder that affects movement and cognition. VPS13A forms a complex with the membrane protein XK to mediate ATP-induced phospholipid scrambling in the plasma membrane. Here, we established a mouse cell system expressing full-length mouse VPS13A and examined its interaction with XK. Mutational analysis revealed that VPS13A binds to XK through a C-terminal β-strand that interacts with a β-hairpin in the central region of XK, an interaction essential for scramblase activity. The XK paralog XKR2, which contains a similar β-hairpin structure, also associates with VPS13A and supports phospholipid scrambling. We analyzed 10 mouse VPS13A variants corresponding to human patient mutations and classified them into 4 groups: (a) L67P, I90K, and W2453R, which showed reduced expression; (b) A1091P and M3080R, which were normally expressed but lacked scramblase activity; (c) S1446P, Q2689H, Y2713C, and R3084H, which modestly impaired expression or activity; and (d) I2763R, which altered cell size and disrupted ER independently of XK. These findings define the VPS13A–XK interaction interface, clarify the functional impact of disease-causing mutations, and reveal an unexpected gain-of-function mutation of a VPS13A variant.

Authors

Xing Lin, Yuta Ryoden, Chigure Suzuki, Hiroyuki Ishikawa, Takaharu Sakuragi, Yasuo Uchiyama, Shigekazu Nagata

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Figure 7

Pathological missense mutations in the mouse VPS13A.

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Pathological missense mutations in the mouse VPS13A. The AlphaFold 3–pre...
The AlphaFold 3–predicted tertiary structure of the mouse VPS13A-XK complex is shown with 6 residues, the missense mutations of which strongly affect protein expression or function. XK is shown in tan with a hairpin structure in orange. VPS13A is colored violet, and the β-strands and α-helix in the N- and C-termini are blue and green, respectively. The essential 6 residues are shown as sphere structures with colored elements.