Undiagnosed child, severly mentally & physically handicapped

My son has been handicapped and undiagnosed since birth.  He is now 4 years old and I have stepped up my efforts to help find a diagnosis, so that I may find a prognosis and fell better about having another child.  I have attached his clinical notes and any thoughts would be much appreciated.

Joshua Colten Quinsey was seen in Pediatric Neurology Clinic on August 6, 2008.  Colten, as you know, is a nearly 4-year-old boy with severe static
encephalopathy and quadriplegic cerebral palsy of unclear etiology, despite
a very extensive workup.  Colten's current medications include baclofen 4
mL 3 times a day; Valium 1 mg per mL, 3 mL t.i.d.; Robinul, Prilosec, and
Singulair.  

Colten underwent MRI of the brain on 6/26/2008 which continues to show delayed myelination, particularly in the centrum seminovale but shows some improvement from last MRI on 3/9/2006.  I reviewed both studies with Colton's mother today.

DEVELOPMENTAL HISTORY
Joshua continues to be profoundly delayed.  He does not hold up his head.
He has minimal control of his arms and legs.  He continues to be quite
spastic.  He is in the Brighton preschool program.  He does some interaction with his environment.

REVIEW OF SYSTEMS
Review of systems is negative for general health, ears, eyes, nose, throat, heart, lungs, gastrointestinal, musculoskeletal, psychiatric, endocrine, or blood problems.

PAST MEDICAL HISTORY
Unchanged.  Colton was a 2.81-kg product of a 38-week gestation, delivered by spontaneous vaginal delivery.  Apgars were 7 at one minute, 8 at five minutes.  He was admitted to the St. Vincent's NICU at approximately 1-1/2 hours of age because of respiratory distress and was intubated for 5 days.  Colton was transferred to Children's Hospital on 9/28/04 for placement of gastrostomy tube.  He had admits in January 2005, October 2005, February 2006, August, 2006 for respiratory distress and in December, 2007 for increased back arching thought to be seizure but was probably opisthotonos.

Prior Neuroimaging
Cranial MRI (December 30, 2004) at the age of 4 months, was officially read as normal although in retrospect there is subtle delay of demyelination
Cranial MRI (March 9, 2006) showed diffuse thinning of the corpus callosum, normal signal intensity in the centrum semi ovale consistent with delay of myelination.    
Head CT (December, 2007) showed some mild increased attenuation of the dorsal thalami that may represent calcifications.
Cranial MRI (6/26/2008) continues to show delayed myelination, particularly in the centrum seminovale but shows some improvement from last MRI on 3/9/2006.  Corpus callosum is still thin and ventriculomegaly is stable.

Other studies
--Swallowing study in March 2005 showed primary aspiration, so Colton is fed by G tube.
--Electrodiagnostic testing (2005) showed that retinal function was normal but no recordable activity was seen in the visual cortex.

Prior EEGs
--Video EEG (11/4/04) showed occasional sharp wave activity over the left hemisphere vertex.
--EEG (December 2004) showed polymorphic delta activity with some multifocal spike wave discharge.  
--EEG (1/3/05) reported to show myoclonic seizures.  Colton had been placed on Valium for episodes of tremor, but then Topamax was added and the episodes of rapid jerks improved markedly.    Topamax was weaned off that in March 2007.  In retrospect, we think that many of his later episodes of jerks were likely related to spasticity.  
--EEG (12/12/2007) captured the episodes of arching, which did not show any evidence of seizure.  However, he did have background slowing and intermittent rhythmic delta activity in the bitemporal regions.  Colten was discharged home on a higher dose of baclofen, and the episodes of arching have improved.

Prior laboratory evaluation
Negative testing for Pelizaeus-Merzbacher disease, MECP2 deletion testing performed at Baylor Lab, normal plasmalogens, normal long chain fatty acids, normal chromosomes, but he has not had telomeres done.  He also had normal urine sialic acid, urine oligosaccharides, and mucopolysaccharide screen.  Negative Prader-Willi screen using FISH.  I do not think he has had DNA methylation probe.  He has also had normal urine organic acids and plasma amino acids.

Colten has undergone several muscle biopsies in conjunction with other procedures.  Frozen muscle has been sent to Center for Inherited Diseases in Energy and Metabolism (CIDEM) at Case Western Reserve University in Cleveland for assessment of mitochondrial disease.  He has had muscle biopsy with G-tube placement in 2004 which was thought to be normal.  Repeat muscle biopsy in summer of 2006 showed decreased activity of some respiratory chain enzymes, but control enzymes are also low, so there is question of whether there is degradation of the sample in shipping.  We then did fibroblast assay for which it took a long time to get the results.  The initial test performed there questioned whether or not there was a deficiency in the pyruvate dehydrogenase complex.  However, when they reassayed the fibroblasts in December 2007, there is no clear evidence of PDC deficiency.  We also had sent off leukocytes for PDC testing with Colten's blood, with my blood as a control, as a non-related control is required by the laboratory.  Both the samples ended up with low PDC activity, which was likely due to shipping problems or handling of the samples rather than truely low in both my blood and his.  I did speak at length on the phone with Dr. Doug Kerr, head of the CIDEM laboratory, and he feels that, although we cannot completely rule out a respiratory chain problem, the likelihood of a mitochondrial problem is low.  He did suggest that we could send off for genetic testing of the PDC complex to Baylor University.  However, it is uncertain what percentage of mutations this testing picks up.  

PAST SURGICAL HISTORY
G-tube with fundoplication and muscle biopsy (9/2004)
Myringotomy (2005)
Myringotomy and muscle biopsy (7/2006)

FAMILY HISTORY
This is the 1st child of Colten's parents.  They have no other children.  We have discussed whether they want more children but they have been concerned about potential risk of having another child with problems similar to Colten.
No family history of developmental delay or seizures.

PHYSICAL EXAMINATION
Weight was 17.3 kg.  Length was not obtained.  Head circumference 46.5.  We have had head circumferences in the past recorded between 46 and 47 cm.   General exam shows him to be alert.  He is interactive with his mom but is clearly profoundly delayed.  He does coo, but otherwise is quite impaired.  HEENT:  Narrow head in frontal-parietal region.  High palate, narrow jaw with crowded teeth.  Lungs were clear to auscultation but have coarse breath sounds.  Heart had a regular rate and rhythm without murmur.  Abdomen was soft and nontender.  G-tube site is dry.  

Neurological examination revealed extraocular movements were intact.
He does not track that well.  He does blink to light. No nystagmus.  Pupils
were equal, round, and reactive to light.  Facial movement was symmetric.
Tongue and palate were midline.  He does have some drooling.  Motor exam
continues to show a severe neck hypotonia.  He has very little control of
his head.  He has increased tone in his arms, elbows, and hands.  He
actually has quite good range of motion in his legs, although there is mild
increased tone in his ankles.  There are no contractures.  Deep tendon
reflexes are 1+ in the biceps, triceps, brachioradialis, and 2+ at the
patella and ankles, with toes downgoing.  He does not have any voluntary
movement of his arms.

IMPRESSION
A 3-year, 11/12 month-old boy with severe static encephalopathy of unclear etiology.  MRI suggests disorder of demyelination but Pelizaeus-Merzbacher disease testing has been negative.