Etymology
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cipher (n.)

late 14c., "arithmetical symbol for zero," from Old French cifre "nought, zero," Medieval Latin cifra, which, with Spanish and Italian cifra, ultimately is from Arabic sifr "zero," literally "empty, nothing," from safara "to be empty;" a loan-translation of Sanskrit sunya-s "empty." Klein says Modern French chiffre is from Italian cifra

The word came to Europe with Arabic numerals. From "zero," it came to mean "any numeral" (early 15c.), then (first in French and Italian) "secret way of writing; coded message" (a sense first attested in English 1520s), because early codes often substituted numbers for letters. Meaning "the key to a cipher or secret writing" is by 1885, short for cipher key (by 1835).

Figurative sense of "something or someone of no value, consequence, or power" is from 1570s.

cipher (v.)

also cypher, 1520s, "to do arithmetic" (with Arabic numerals), from cipher (n.). Transitive sense "reckon in figures, cast up" is from 1860. Meaning "to write in code or occult characters" is from 1560s. Related: Ciphered; ciphering.

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Definitions of cipher
1
cipher (n.)
a message written in a secret code;
Synonyms: cypher
cipher (n.)
a mathematical element that when added to another number yields the same number;
Synonyms: zero / " / nought / cypher
cipher (n.)
a quantity of no importance;
Synonyms: nothing / nil / nix / nada / null / aught / cypher / goose egg / naught / zero / zilch / zip / zippo
cipher (n.)
a person of no influence;
Synonyms: cypher / nobody / nonentity
cipher (n.)
a secret method of writing;
Synonyms: cypher / cryptograph / secret code
2
cipher (v.)
convert ordinary language into code;
Synonyms: code / encipher / cypher / encrypt / inscribe / write in code
cipher (v.)
make a mathematical calculation or computation;
Synonyms: calculate / cypher / compute / work out / reckon / figure
From wordnet.princeton.edu