This may explain it.
The father's gene,
http://globin.cse.psu.edu/html/huisman/thals/beta/Codon.39.(C-@T)..CAG(Gln)-@TAG(stop.codo.htmlMUTATION Codon 39 (C->T); CAG(Gln)->TAG(stop codon)
AMINO ACID REPLACEMENT None
TYPE OF BETA-THAL beta°
MECHANISM This mutation changes codon 39 into a stop codon terminating translation
IDENTIFICATION Cloning of the beta-globin gene; amplification of the beta-globin gene and sequencing; dot-blot analysis; ARMS; gene mapping with MaeI
HEMATOLOGY IN HETEROZYGOTE(S) Typical for beta°-thal with low MCV and MCH values; microcytosis; hypochromia (n=10): Hb 11.1±1.35 g/dl; MCV 72.6±8.5 fl; MCH 20.2±1.1 pg; Hb A2 4.85±0.5%; Hb F 1.25±1.0% (Ref. 4)
HEMATOLOGY IN HOMOZYGOTE(S) Severe transfusion-dependent beta-thal
Your gene
http://globin.cse.psu.edu/html/huisman/thals/beta/12.620.bp.deletion..the.Dutch.deletion.htmlMUTATION 12,620 bp deletion (see Fig. 4); the Dutch deletion
AMINO ACID REPLACEMENT None
TYPE OF BETA-THAL beta°
MECHANISM No beta chain production; considerable increase in gamma chain formation
IDENTIFICATION Gene mapping; cloning; amplification; DNA sequencing
HEMATOLOGY IN HETEROZYGOTE(S) Hb 12.4-13.0 g/dl; MCV 65-70 fl; MCH 18-24 pg;
Hb A2 6.8, 5.9, 6.3, 6.0, 6.4, 8.6, 5.1, 6.5, 5.9, 5.5, 6.1%;
Hb F 8.0, 10.7, 6.7, 10.4, 4.6, 4.1, 9.4, 5.9, 5.5, 7.7, 10.9%
HEMATOLOGY IN HOMOZYGOTE(S) Two homozygotes: Hb 10.9, 13.1 g/dl; MCV ~73 fl; MCH 20-25 pg; Hb A2 2.0, 2.4%; Hb A 0%; Hb F 98.0, 97.6%
The Dutch beta zero deletion allows for a compensation by the gamma gene, resulting in a high production of HbF. This is a characteristic of some of the beta zero thalassemias. It seems the Dutch deletion results in high expression from the gamma gene. This is explained in this article excerpt
http://www.mendeley.com/research/filipino-beta-zero-thalassaemia-high-hb-a2-beta-zero-thalassaemia-resulting-large-deletion-5-beta-globin-gene-region/A large novel deletional beta zero thalassaemia mutation associated with unusually high levels of haemoglobin (Hb) A2 in heterozygotes is described in two unrelated subjects of Filipino background. The deletion was characterised by DNA mapping including pulsed field gel electrophoresis. Filipino beta zero thalassaemia extends for approximately 45 kb beginning approximately 1.5 kb 3' to the delta globin gene. It is the largest deletion to date which gives rise to the beta zero thalassaemia phenotype. This mutation, similar to previously described deletional beta zero thalassaemias associated with high Hb A2, removes sequences 5' to the beta globin gene promoter and emphasises the functional importance of the 5' beta globin region in eliciting the unusually high level of Hb A2. This example also suggests that it is the 3' sequences which are transposed rather than the actual deletion size which are significant in the raised fetal haemoglobin (Hb F) found with some of the thalassaemias.
The full article can be read at
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1016308/Because the other gene deletion offers no compensation it may be too early to predict the long term outcome. I tend to think this will manifest as intermedia and transfusion might be avoided if fetal hemoglobin production stays at such a high rate. Because of his relatively young age, it is not yet predictable, but being that he is 2 years old and carries a hemoglobin level more associated with thal minor, it is a good sign. Intermedia is simply a classification and basically means the genes say major, but either the genes are + and do produce enough adult hemoglobin to survive without transfusion, or are zero and some other factor compensates in some way, such as in the described cases where a large deletion actually allows for higher activity of the gamma gene, allowing gamma globin to combine with alpha globin, producing unusually high fetal hemoglobin. Because there is a better balance of globins, this also greatly reduces the amount of unmatched alpha globin. This is far more important than one may realize, as the damage these unmatched alpha chains cause in beta thal is great.
So, it appears that the same effect is realized as with HPFH, even though that is not the reason. It is amazing but two of the Dutch deletion can result in a normal hemoglobin level. "HEMATOLOGY IN HOMOZYGOTE(S) Two homozygotes: Hb 10.9, 13.1 g/d" Even with no beta globin produced, a hemoglobin range as high as 13 is observed.
I don't know if it can help even more because the HbF level is already so high, but he may be helped by natural methods like wheatgrass extract and resveratrol supplements. Both show some ability to raise HbF levels in people with active gamma genes. Both also have positive properties than can be of benefit in thalassemia. I don't know if I would go the hydroxyurea route for raising HbF unless his total Hb drops into a range where transfusions might be considered. Because he has shown a good ability to produce HbF, he would be a good candidate for hydroxyurea therapy if his Hb drops to the 6-7 range. Folic acid, B complex and vitamin E are all recommended.
Do you also have a high HbF level?