Phoebe:
First off take a deep breath - you can have bad years (indeed a series of bad years) and it can all come good in the end.
Expected progress through NC Levels according to MN is: www.mumsnet.com/learning/assessment/progress-through-national-curriculum-levels - see table on bottom
So in theory your DC should be working to NC L3b by the end of Y4.
I think the school are looking at the fact he'll be tracked as a higher achiever at the end of KS1 (with those NC Level 3s) - so should be on track for NC L5 work in Year 6.
Math in KS2 really does rely on sound knowledge of multiplication facts - so the first question to ask yourself is how is DC's times tables? Can he instantly tell you 4 x 9 = 36 or 36 divided by 4 = 9. If not - that's the obvious place to put in more time. Not necessarily your own - there are tons of video games out there that will provide all sorts of practise (without feeling like work). The new requirement is that by end Y4 - all times tables x0 through x12 should be mastered.
Lots of multiplication feeds on MN - just search and you'll get lots of good tips.
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Reading - moves from functionally being able to read out loud (which is initially rewarded) - to being able to understand deeper meaning of the text - motivation of characters/ elements of plot/ utlimately you may even discuss literary devices or author's writing style. If you're still reading from a guided reading series - there usually are comprehension questions at the back of the book - which you can use to discuss the story.
I spent a lot of time at this point discussing meaning of words - as DD1 often would read them beautifully but had no clue what they meant. So discussing meaning of words/ how choice of words can be important (making something more spooky or mysterious, etc...).
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writing is always tricky - but be sly - encourage thank you cards for presents/ post cards when on holiday/ making comics. When there is written work for homework - be a stickler that they don't do the bare minimum. It really does them no favours.
Every spring I think CBBC has a children's writing competition. You can also write in to authors for various series - often getting nice goody packs.
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DD1 really struggled until mid Y4 and it all came good. So don't despair or give up hope. The key for us was doing a bit each week toward mastering multiplication tables/ improving reading skills and keeping writing juices flowing (we had very little homework to speak of at all). It does all add up - and really makes a difference.
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Finally don't keep silent - talk to friends about what they're doing at home - I only found out very late in Y6 how much extra work many parents were doing at home (preparing for the 11+ with workbooks/ hiring tutors for the 11+/ getting in extra workbooks/ doing on-line tutorials/ etc....) - if that is playing out as well at your school - and you're not doing a lot at home - that may well explain why to the teachers it seems your son is standing still and others are racing ahead.
HTH