disease a person is born with (including genetic disorders presenting within 6 months)

Genetic disorders are the most common cause
22q13 deletion syndrome a.k.a. Phelan–McDermid syndrome
3-Methylcrotonyl-CoA carboxylase deficiency
Achondroplasia
Aicardi syndrome
Autism spectrum disorders
Canavan disease
Centronuclear myopathy (including myotubular myopathy)
Central core disease
CHARGE syndrome
Cohen syndrome
Costello syndrome
Dejerine–Sottas disease (HMSN Type III)
Down syndrome a.k.a. trisomy 21 — most common
Ehlers–Danlos syndrome
Familial dysautonomia (Riley–Day syndrome)
FG syndrome
Fragile X syndrome
Griscelli syndrome Type 1  (Elejalde syndrome)
Holocarboxylase synthetase deficiency / Multiple carboxylase deficiency
Krabbe disease
Leighs disease
Lesch–Nyhan syndrome
Marfans syndrome
Menkes syndrome
Methylmalonic acidemia
Myotonic dystrophy
Niemann–Pick disease
Nonketotic hyperglycinemia (NKH) or Glycine encephalopathy (GCE)
Noonan syndrome
Neurofibromatosis
Patau syndrome a.k.a. trisomy 13
Pituitary dwarfism/growth hormone deficiency(in adults)
Prader–Willi syndrome
Rett syndrome
Septo-optic dysplasia (de Morsier syndrome)
Snyder–Robinson syndrome (SRS)
Spinal muscular atrophy (SMA)
Succinic semialdehyde dehydrogenase deficiency (SSADH)
Tay–Sachs disease
Werdnig–Hoffmann syndrome – Spinal muscular atrophy with congenital degeneration of anterior horns of spinal cord. Autosomal recessive 
Wiedemann–Steiner syndrome
Williams syndrome
Zellweger syndrome a.k.a. cerebrohepatorenal syndrome
Developmental disability
Cerebellar ataxia (congenital)
Sensory processing disorder
Developmental coordination disorder
Hypothyroidism (congenital)
Hypotonic cerebral palsy
Teratogenesis from in utero exposure to Benzodiazepines

Acquired
Acquired – i.e. onset occurs after birth

Genetic
Muscular dystrophy (including Myotonic dystrophy) – most common
Metachromatic leukodystrophy
Rett syndrome
Spinal muscular atrophy
Infections
Encephalitis
Guillain–Barré syndrome
Infant botulism
Meningitis
Poliomyelitis
Sepsis
Toxins
Infantile acrodynia (childhood mercury poisoning)
Autoimmunity disorders
Myasthenia gravis – most common
Abnormal vaccine reaction
Celiac disease
Metabolic disorder
Hypervitaminosis
Kernicterus
Rickets
Neurological
Traumatic brain injury, such as the damage that is caused by shaken baby syndrome
Lower motor neuron lesions
Upper motor neuron lesions
Miscellaneous
Central nervous system dysfunction, including cerebellar lesions and cerebral palsy
Hypothyroidism
Sandifer syndrome
Neonatal benzodiazepine withdrawal syndrome in children born to mothers treated in late pregnancy with benzodiazepine medications

Diagnosis
The approach to diagnosing the cause of hypotonia (as with all syndromes in neurology) is first localization.
Less common modes of transmission include vertical transmission, which is transmission from mother to child during pregnancy or at birth. Transmission via infected blood products and through organ donation is also theoretically possible during times of outbreak, though no cases have yet been documented. The incubation period ranges from one to twelve days, and is most typically three to seven.Chikungunya is related to mosquitoes, their environments, and human behavior. The adaptation of mosquitoes to the changing climate of North Africa around 5,000 years ago made them seek out environments where humans stored water. Human habitation and the mosquitoes environments were then very closely connected. During periods of epidemics humans are the reservoir of the virus. Because high amounts of virus are present in the blood in the beginning of acute infection, the virus can be spread from a viremic human to a mosquito, and back to a human. During other times, monkeys, birds and other vertebrates have served as reservoirs. Three genotypes of this virus have been described, each with a distinct genotype and antigenic character: West African, East/Central/South African, and Asian genotypes. The Asian lineage originated in 1952 and has subsequently split into two lineages – India (Indian Ocean Lineage) and South East Asian clades. This virus was first reported in the Americas in 2014. Phylogenetic investigations have shown that there are two strains in Brazil – the Asian and East/Central/South African types – and that the Asian strain arrived in the Caribbean (most likely from Oceania) in about March 2013.