question #1： they did find one mutation but they ruled out that the mutation (or you can call it a variation, a SNP,  but it is a cSNP and it changed amino acid sequence) was the cause.  It is quite risky to rule out that SNP from my point of view, because they cited heterozygosity rate 0.47 (2pq) and minor allele frequency 0.37 (q=0.37, remember the hardy-weinberg equilibrium in genetics？), they do not show homozygous minor allele genotype (you can calculate it out, q square=0.137, meaning in the population there will be only 13.7% people are homozygous minor allele!). and all cases have that SNP, it is a big risk to rule it out. --the reviewer apparently does not know much about population genetics. 



question #2: amyloid is a very different problem in biology, the protein folding is the key, usually not due to any mutations.  the fibril formation is also NOT dependent on the amino acid sequence, --I have not kept up with the literature and not sure whether people know the cause of amyloid or not.



question #3: even thought the protein aa sequence has no change, it does not mean the regulatory sequence are not changed, such as promoter region and 3'-UTR regions.  These regions play key roles in regulating gene expression. 



question #4: to answer your pre-mRNA splicing question, you are right, only look at gDNA will miss possible alternative splicing sites; and fragments of protein may be missing.  if you google you may find some online software to tell you possible alternative splicing sites on that DNA sequence.  if there are such alternative splicing, you should also be able to find them in NCBI gene database --just go to ncbi site, select "nucleotide" in the box, search "human lect2“， you may find a number of entries.  



give you a reference for amyloid: 

Exp Dermatol. 2015 Mar; 24(3): 171–174.