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Grammar detail: 損ねる(そこねる)

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JLPT:
損ねる(そこねる) - miss (something); fail (to do something)
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verb stem
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そこ
ねる
means
miss the chance to do ~; fail to do ~
 
かれ
その
れっしゃ
列車
りそこねた

They missed the train.
そこ
ねる (also commonly written with kana only as そこねる) is a transitive verb meaning 'to harm' or 'to injure'. The implication here is that some action has been 'injured' or has otherwise failed.
This form is commonly used with several verbs, for example:
ねる write incorrectly
ねる fail to say; be unable to say
ねる fail to hear (not mishear)
ねる overlook (something); miss something (eg a game); misjudge (someone)
そこ
なう, the intransitive form, can also be used in this construction. The change in meaning is subtle: the transitive form implies a more literal physical failure to do something, whereas the intransitive is both figurative and literal.
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Words used in this grammar

1. to harm; to hurt; to injure; to damage
auxiliary verb
2. to fail in doing
(click the word to view an additional 2 forms)
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ichidan verb, transitive verb
1. to harm; to hurt; to injure; to wreck
auxiliary verb
2. to miss one's chance to (do something); to fail to (do what one ought to have done)
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Kanji used in this grammar

ソン   そこなう    そこねる to injure, to harm   
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ショ   か to write   
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ゲン   ゴン   say; word   こと word, saying   い to say   
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2
ブン   モン   き to listen, to hear   きこえる to be heard   
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1
ケン   み to see   みえる to be seen; to appear   みせる to show   
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1
ヒ   かれ he   
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3
レツ    row   
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3
シャ   くるま car   
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ジョウ   load; power   の to board   のせる to load on   
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3
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