I'm not a teacher, I am a speech and language therapist and I am only offering my opinion and very general advice - Please do not interpret this as a diagnosis would not want to give specific advice without meeting and assessing your son.
However, from what you are saying it sounds as if he might have some difficulties with his phonological awareness skills ( knowledge phoneme, syllable, rhyme awareness) morphological awareness skills (understanding and use of word parts that carry significance. For example, root words, prefixes, suffixes, and grammatical inflections (e.g., -s or –es for plurals)
This is not unusual, but it makes learning to read via synthetic phonics (print-to-speech, sounding out) very tricky! and exhausting for your son I would imagine.
So very simply, synthetic phonics works by showing the letter or digraph
e.g. th and talking about the sounds that letter can make in different word contexts - voiceless/voiced dental fricative
Alternative methods which might be more suitable for your son, teach orthographic pattern knowledge via sound to print e.g.
/k/ voiceless velar stop - can be written as K, C, CK, CC, KK
Alongside other skills such as -
*Phonological Awareness - focusing on auditory processing and sound perception
*Morphological Awareness & Knowledge
*Semantic & Vocabulary Knowledge
*Mental Images of Words
I won't go into masses of detail but very basically, the brain is biologically wired only for oral language—speaking, listening, and understanding—not for written language - reading and writing.
There are no genes specific to reading and writing. There are no neurological or biological structures specific to reading and writing.
In order to successfully read and write, each brain must “re-purpose” regions biologically designed for other purposes and create new circuits and neural connections. As well as that we expect children to develop automaticity for retrieving representations within the structures and efficiency in the connections among those structures. There's a lot going on!
If you are still concerned I would seek advice from a speech and language therapist that specialises in literacy development.