Crypt opens with a cluster English cannot really pronounce, and that is a Greek signature. The word is Greek krypte, "a vault," short for krypte kamara, "hidden vault," from kryptos, "hidden." English took it in the early 1400s through Latin crypta, meaning a grotto or cavern; the sense of an underground burial vault in a church only dates from 1789.
The y is the other Greek marker here. In the middle of a word, a y that works as a vowel almost always transliterates the Greek letter upsilon — myth, system, syntax, hymn, crypt. Native English words use i in that position. Between the y and the initial cluster, crypt is about as legibly Greek as a five-letter word can be, even though the Greek etymology itself is uncertain enough that some scholars think the word was borrowed into Greek from something older.
crypt (n.) early 15c., cripte , "grotto, cavern," from Latin crypta "vault, cavern," from Greek krypte "a vault, crypt" (short for krypte kamara "hidden vault"), fem. of kryptos "hidden," verbal adjective from kryptein "to hide," which is of uncertain origin. Comparison has been made to Old Church Slavonic kryjo , kryti "to hide," Lithuanian kráuti "to pile up." Beekes writes that krypto "is formally and semantically reminiscent of [ kalypto ]; the verbs may have influenced each other." For this, see calypto- . But he adds, "However, since there is no good IE etymology, the word could be Pre-Greek." Meaning "underground burial vault or chapel in a church" is attested by 1789. also from early 15c.
crypt came in through Greek, and its spelling follows that family's conventions.
How that family writes these sounds
| short /i/ in the middle | y, transliterating υ, where a native word would use imyth, system, syntax, crypt |
What gives it away on the page
| y as a vowel in the middle | Transliterates υ. Native words use i here.myth, system, physics, syntax, crypt |