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My gut feeling is that Duchenne muscular dystrophy will be high up the list, along with other X-linked disorders (X-linked ichthyosis is reasonably common and often due to new mutations; fragile X syndrome is also reasonably common and the disease-causing mutation often occurs through expansion of a premutation allele, which is sort of a new mutation). The list might also include achondroplasia, simply because of the very high new mutation rate, and autosomal dominant polycystic kidney disease which is relatively frequent and caused by new mutations 10% of the time.

Prevalence of some single gene disorders[1]
Disorder Prevalence
Autosomal dominant
Familial hypercholesterolemia 1 in 500
Polycystic kidney disease 1 in 1250
Huntington disease 1 in 2,500
Hereditary spherocytosis 1 in 5,000
Marfan syndrome 1 in 20,000
Autosomal recessive
Sickle cell anemia 1 in 625
(African Americans)
Cystic fibrosis 1 in 2,000
(Caucasians)
Tay–Sachs disease 1 in 3,000
(American Jews)
Phenylketonuria 1 in 12,000
Mucopolysaccharidoses 1 in 25,000
Glycogen storage diseases 1 in 50,000
Galactosemia 1 in 57,000
X-linked
Duchenne muscular dystrophy 1 in 7,000
Hemophilia 1 in 10,000
Values are for liveborn infants

Disorder

Frequency per 1000 births

Autosomal dominant


Familial combined hyperlipidaemia


5.0

Familial hypercholsterolaemia


2.0

Dominant otosclerosis


1.0

Adult polycystic kidney disease


0.8

Multiple exostoses


0.5

Huntington's disease


0.5

Neurofibromatosis


0.4

Myotonic Dystrophy


0.2

Congenital spherocytosis


0.2

Polyposis coli


0.1

Autosomal recessive


Cystic fibrosis


0.4

alpha-1-antitrypsin deficiency


0.2

Phenylketonuria


0.1

Congenital adrenal hyperplasia


0.1

Spinal muscular atrophy


0.1

Sickle cell anaemia


0.1

beta-Thalassaemia


0.05

X-Linked recessive


Fragile X syndrome


0.5

Duchenne muscular dystrophy


0.3

X-linked ichthyosis


0.2

Haemophilia A


0.1

Becker muscular dystrophy


0.05

Haemophilia B


0.03

  1. ^ Table 7-1 in:Mitchell, Richard Sheppard; Kumar, Vinay; Abbas, Abul K.; Fausto, Nelson (2007). Robbins Basic Pathology. Philadelphia: Saunders. ISBN 1-4160-2973-7.{{cite book}}: CS1 maint: multiple names: authors list (link) 8th edition.