Chapter 170. Key Principles in Human Genetics

Genetic disorders and birth defects are sometimes perceived as being so uncommon that the general pediatrician will seldom encounter them. However, each day more than 400 babies with birth defects are born in the United States, and 1 of every 5 infant deaths is caused by these disorders. Virtually every medical condition, except for some cases of trauma, is influenced by an individual’s genetic background. Rapid advances in our knowledge of the genetic basis of disease, coupled with emerging technologies for high-throughput genetic testing, are also rapidly transforming the practice of medicine.

Comprehensive databases of factual information about the identification of new disease genes, genotype–phenotype correlation, and the availability of genetic testing have become widely available online and in published review articles. Thus, each of the following sections seeks to emphasize important fundamental concepts while providing paradigmatic examples.

Traditionally, various human traits (eg, skin color, intelligence) and disorders (eg, phenylketonuria, achondroplasia) have been divided into those that are genetic versus those that are nongenetic, the latter usually referring to disorders “determined” by the environment (eg, infectious diseases, teratogens). However, this dichotomy separating gene and environment is largely artificial, and the distinction between the two has become increasingly blurred. Disorders caused by mutations in a single gene (eg, cystic fibrosis, sickle-cell disease) can be heavily influenced by the environment, and diseases caused by the environment (eg, AIDS secondary to infection with HIV-1) can be substantially modified by the presence of certain polymorphisms. In other words, the cause of most diseases can be considered genetic and environmental; some diseases are more strongly influenced by genes, whereas others are more strongly influenced by the environment.

Whether defined narrowly or broadly, genetic disorders and birth defects contribute substantially to morbidity and mortality in pediatric patients. For example, the percentage of deaths attributable to genetic disease in hospitals in the United Kingdom has risen from 16.5% in 1914 to 50% in 1976. Birth defects are also the leading cause of death in infancy in the United States, accounting for more than 20% of infant deaths. Cardiovascular malformations are the leading cause of premature mortality from congenital anomalies. This reflects a better understanding of the etiology of pediatric diseases as well as the substantial reduction in infectious disease and perinatal mortality during the 20th century. Population-based studies suggest that birth defects and genetic disorders account for about 10% of hospitalizations and about 30% of all hospitalization charges. Approximately 7% of pediatric admissions are for single-gene and chromosomal disorders, and another 15% to 20% for congenital malformations of different types. Moreover, about 35% of hospital deaths of children are caused by a genetic condition and/or birth defect. Recent advances in therapeutics have substantially prolonged the survival of children with birth defects and/or genetic diseases, challenging practitioners to care for older children and young adults with genetic disorders.

Classifications of genetic disorders depend, in part, on the delineation of a phenotypic trait (eg, mental retardation, craniosynostosis) and the judgment of whether this trait varies substantially from a “normal” trait. Whether a trait should be considered normal or abnormal (eg, a midline abdominal aorta, short digits) is not always clear, and the decision may depend, in part, on findings in other family members. Genetic disorders can be broadly classified into several major groups: chromosome disorders, single-gene disorders, multifactorial disorders, and disorders with nontraditional mechanisms of expression and inheritance.

Chromosome disorders result from abnormalities of chromosome number (ie, aneuploidy) and/or structure. These abnormalities include duplications, deletions, rearrangements, extra chromosomes (trisomy), and missing chromosomes (monosomy). Most chromosome disorders arise de novo and are not transmissible. However, some chromosome disorders are heritable because they are carried by an unaffected parent in a state that does not cause disease (eg, balanced rearrangements) but can be transmitted to an offspring to produce a state that does cause disease (unbalanced rearrangement). Most conceptions with chromosome abnormalities are terminated spontaneously early in gestation, and chromosome abnormalities are the leading known cause of pregnancy loss. Most individuals with chromosome disorders have major and/or minor malformations, variable degrees of mental retardation, and/or growth deficiency.

Disorders in which single genes have been altered are called monogenic conditions. Single-gene disorders can be transmitted from parent to offspring in autosomal-dominant or autosomal-recessive patterns and thus are sometimes known as mendelian conditions. Single-gene disorders can also be produced by new mutations in a single individual that are appearing for the first time in a family; the mutation has arisen de novo in the affected family member. Copies of genes that have different sequences are referred to as alleles. A gene’s location on a chromosome is termed a locus.

The four modes of inheritance of single-gene disorders are autosomal-recessive, in which both copies of a gene at a single locus on an autosome (nonsex chromosome) are altered; autosomal-dominant, in which only one allele of a gene at a single locus on an autosome is altered; X-linked recessive, in which one allele of a gene at a locus on the X chromosome is altered in affected males and both alleles of a gene at a locus on the X chromosome are altered in affected females; and X-linked dominant, in which one allele of a gene at a locus on the X chromosome is altered in affected males and females. Y-linked inheritance is uncommon for genetic disorders.

Substantial progress has been made toward identifying the genes that cause single-gene disorders. However, these conditions represent only a small fraction of the total burden of genetic disease. Most birth defects are not caused by alterations of a single gene or chromosome, and many common pediatric disorders are influenced by different combinations of alleles at various loci. Traits in which variation is caused by the effects of many different genes are called polygenic. If the variation of a polygenic trait is also affected by nongenetic factors (eg, environmental variables), the terms multifactorial or complex are often used to describe the trait. In contrast to single-gene disorders, multifactorial traits are not transmitted in mendelian patterns. The identification of the genetic and environmental determinants of multifactorial traits is a major objective of genetic research.

Some genetic disorders do not segregate in the patterns expected of single-gene conditions or multifactorial traits and are transmitted from parent to offspring in nontraditional patterns of inheritance. Disorders exhibiting nontraditional patterns of inheritance include those caused by mutations in the mitochondrial genome, uniparental disomy (two alleles from the same locus inherited from one parent instead of both parents), and gene duplication. The expression of some conditions is influenced substantially by whether the altered allele is transmitted to a child by the mother or father, a so-called parent-of-origin effect. Some genetic conditions exhibit a nontraditional pattern of inheritance as a consequence of this parent-of-origin effect and are relatively uncommon.

The terms congenital, hereditary, and familial are not synonymous. Conditions that are present at birth are referred to as congenital conditions, whether the major risk factor is genetic or not. For example, infection with cytomegalovirus, clubfeet caused by oligohydramnios, and trisomy 21 are all congenital conditions. However, only trisomy 21 is clearly a genetic condition, and none of these conditions are usually hereditary.

The term hereditary defines conditions that can be transmitted from parent to offspring. All hereditary conditions are genetic conditions, but not all genetic conditions are hereditary (eg, most cases of trisomy 21). Conditions that appear to cluster within families are frequently called familial conditions and may include nongenetic conditions (eg, rotaviral or streptococcal infections) as well as genetic conditions. Nevertheless, although all hereditary conditions can be familial, not all genetic conditions are familial (eg, most cases of trisomy 21). Distinguishing which term most appropriately defines a condition facilitates diagnosis, management, and counseling of families about the risk of recurrence of a condition.

The probability that an individual who possesses a disease-related genotype (an individual’s allelic constitution at a single locus is called a genotype) exhibits the disease phenotype is called penetrance. When this probability is less than 1, the disease is said to exhibit reduced (or incomplete) penetrance. Penetrance levels are usually estimated by examining a large number of families and determining what proportion of the obligate carriers (ie, those individuals who have an affected parent and an affected child and thus must be carriers of the altered gene) or obligate homozygotes (in the case of autosomal-recessive disorders) develop the disease phenotype. Retinoblastoma is a good example of a genetic condition in which reduced penetrance is observed. Family studies have demonstrated that about 10% of obligate carriers of a mutation in the retinoblastoma susceptibility gene do not develop a retinoblastoma. The penetrance of the condition is thus about 90%.

Individuals with the same genetic condition or even the same genotype can have substantially different phenotypes. This is called variable expressivity. For example, within the same kindred, one sibling with neurofibromatosis type 1 (NF1) may have café au lait spots, axillary freckling, and sphenoid wing dysplasia, and another sibling with NF1 has café au lait spots, a plexiform neurofibroma, and pseudarthrosis of the tibia. Although each sibling has the same genotype, the expression of the NF1 phenotype is different between them.

Variable expressivity may be explained by the influence of other genes (ie, modifying genes), environmental factors (eg, earlier palliative intervention), or random variation. Variable expressivity among families is sometimes related to the presence of different genotypes. The causation of a disease phenotype by a variety of different genotypes at the same locus is called allelic heterogeneity. A potentially powerful strategy to provide affected individuals with better anticipatory guidance is to estimate the correlation between genotypes and specific phenotypic characteristics (genotype-phenotype correlation studies). The compilation of findings from many individuals with a genetic condition defines the distribution of phenotypic variation of a disorder. Although not every affected individual will have the same findings, variable expressivity is often confused with reduced penetrance. The absence of a disease phenotype in an obligate carrier (ie, reduced penetrance) is not considered variable expression of the condition.

Genes that have more than one discernible effect on the phenotype are said to be pleitropic. A good example of a gene that has pleiotropic effects is the cystic fibrosis transmembrane regulator(CFTR). CFTR encodes a protein that forms cyclic-AMP–regulated chloride ion channels that span the cell membrane of specialized epithelial cells such as those that line the lungs and bowel. Mutations in CFTR result in abnormalities of the lungs, pancreas, and sweat glands. Other examples of genetic conditions that result from mutations in genes with pleiotropic effects include Marfan syndrome (characterized by ocular, cardiovascular, and skeletal defects) and osteogenesis imperfecta, in which the bones, teeth, and sclerae are affected. Thus pleiotropy can be caused by genes whose products play similar roles in different tissues and organs. Pleiotropy can also be caused by genes whose protein products play varied roles in different developmental programs. For example, individuals with campomelic dysplasia have a skeletal dysplasia that is sometimes accompanied by sex reversal. Campomelic dysplasia is caused by mutations in a gene called SRY-related HMG-BOX 9 (SOX9), which plays an important regulatory role in skeletal development and sexual differentiation.

Some genetic conditions seem to display an earlier age of onset and/or more severe expression in the more recent generations of a pedigree. This effect is called anticipation. Some investigators had proposed that anticipation was an artifact of better observation and diagnostic tools available to the contemporary clinician: a disorder previously diagnosed at age 60 might now be diagnosed at age 40. Within the past 10 years, it has been demonstrated that for some disorders, anticipation has a biological basis. One of the best examples of anticipation comes from studies of myotonic dystrophy (DM), the most common muscular dystrophy that affects adults. Myotonic dystrophy is characterized by progressive deterioration of skeletal muscle, cardiomyopathy, testicular atrophy, and cataracts and is caused most often by mutations in a gene on chromosome 19 that encodes a protein kinase. Analysis of this gene has demonstrated that myotonic dystrophy is caused by the expansion of a CTG repeat in the 3' untranslated region of the gene (ie, a region transcribed into mRNA but not translated into protein). Unaffected individuals have 5 to 30 copies of the repeat; mildly affected individuals may have 50 to 100 copies of the repeat; and severely affected individuals may have 100 to more than several thousand repeats. The number of repeats is positively correlated with the severity of the disease. Furthermore, the number of repeats often increases with succeeding generations, which have more severe disease compared to preceding generations.

Autosomal-Dominant Disorders

For autosomal-dominant conditions, the presence of only one copy of an altered allele at a locus is sufficient to produce a disease phenotype. Genetic disorders that are inherited in an autosomal-dominant pattern are the most common single-gene disorders described in humans. Individually, however, each autosomal-dominant disorder is relatively uncommon. Thus, most affected offspring are produced from the mating of an affected parent and an unaffected parent or from a de novo mutation. A parent affected with an autosomal-dominant disorder can transmit either the normal or altered allele to his or her offspring. Each of these events has a probability of 0.5. Thus, on average, half of the children will be heterozygous for the altered allele and express the disease, and half will be homozygous for a normal allele. Matings between individuals affected by the same autosomal-dominant disorder are rare.

An idealized pedigree for autosomal-dominant inheritance (Fig. 170-1) illustrates several important characteristics: First, the two sexes exhibit the trait in approximately equal proportions, and males and females are equally likely to transmit the trait. Second, no generation is skipped. Every individual with the trait has an affected parent. Third, father-to-son transmission is observed. Although father-to-son transmission is not required to establish autosomal-dominant inheritance, its presence excludes some other modes of inheritance (eg, X-linked and mitochondrial). Last, an affected individual transmits the trait to half of her or his offspring, on average.

De novo mutations are an important cause of autosomal-dominant conditions. For autosomal-dominant conditions that are lethal in prereproductive age (eg, thanatophoric dysplasia), de novo mutations are the most common cause of the disorder. For some autosomal-dominant conditions (eg, achondroplasia, Marfan syndrome) the age of the father and the likelihood of transmitting a new mutation to his offspring are positively correlated. Sometimes, clearly unaffected parents have more than one child affected with an autosomal-dominant disorder. Recent studies have demonstrated that one of the parents in such families has two or more different cell lines in his or her germ cells (cells that produce sperm or eggs)—with at least one cell line containing an altered allele. This phenomenon is called germ-line mosaicism. Germ-line mosaicism appears to be much more common for some disorders (eg, osteogenesis imperfecta) and is another cause of autosomal-dominant conditions that are lethal in prereproductive age. Two or more cell lines can also be found in the somatic cells of an individual (somatic mosaicism). Individuals with somatic mosaicism may have all the same characteristics found in affected individuals, exhibit abnormalities limited to only tissues containing the mutant cell line, or appear unaffected.

Autosomal-Recessive Disorders

For autosomal-recessive conditions, the presence of two copies of an altered allele at a locus is required to produce a disease phenotype. Genetic disorders that are inherited in an autosomal-recessive pattern are less common than autosomal-dominant disorders in most populations. However, heterozygous carriers for recessive conditions are much more common than affected homozygotes. Thus the parents of individuals affected with autosomal-recessive conditions are usually heterozygous carriers. For example, the prevalence of cystic fibrosis is approximately 1 in 2500 in northern European populations. The Hardy-Weinberg law states that population frequencies of genotypes can be predicted on the basis of gene frequencies in a randomly mating population (random mating is also referred to as panmixia). Suppose that at a two-allele locus, the frequency p of an allele A is 0.70. Then 70% of the sperm and egg cells in a population have this allele. Because the sum of allele frequencies at a locus must equal 1, the frequency q of the allele a is equal to 1 – p = q or 1.0 – 0.7 = 0.3. Under panmixia the probability that a sperm carrying allele A unites with an egg carrying allele A is p × p = p2 or 0.7 × 0.7 = 0.49 (multiplication rule). This is the probability of producing an offspring with the AA genotype. The probability of producing an offspring with the aa genotype is q × q = q2 or 0.3 × 0.3 = 0.09.

Heterozygotes can be produced two different ways. A sperm carrying allele A can unite with an egg carrying allele a, or a sperm carrying allele a can unite with an egg carrying allele A. Thus, the frequency with which this occurs is equal to the product of the gene frequencies, p × q. Because we want to know the overall probability of either event, we use the addition rule, adding the probabilities to obtain a heterozygote frequency of pq + pq = 2pq. Overall, the genotype frequencies of a two-allele locus are equal to p2 + 2pq + q2 = 1. This relationship indicates that the gene frequency (q) for alleles causing CF is equal to q1/2 or (1/2500)1/2 or 1/50. The frequency of normal alleles, p, is (2499/2500)1/2 or approximately 1. The frequency of heterozygotes (2pq) is equal to 2(1)(1/50) = 1/25. Thus, the frequency of heterozygous carriers is approximately 100 times higher than the frequency of affected individuals.

The probabilities of two carriers producing children with two normal alleles (homozygous normal), a normal allele and a disease-causing allele (heterozygous carriers), or two disease-causing alleles (homozygous affected) are 0.25, 0.5, and 0.25, respectively. Thus, on average, one quarter of the children produced by heterozygous carriers will be affected with an autosomal-recessive condition. If a child is known not to be affected, the likelihood that he or she is a carrier is 2:3, ie, likelihood of being a heterozygous carrier (0.5) divided by the likelihood of being a heterozygous carrier (0.5) plus the likelihood of being homozygous normal (0.25).

An idealized pedigree for autosomal-recessive inheritance (Fig. 170-2) illustrates several important characteristics: First, autosomal-recessive disorders are usually observed in one or more siblings but are not usually found in other generations. Second, similar to autosomal-dominant conditions, males and females are affected in equal proportions, and males and females are equally likely to transmit the disease-causing mutation. Third, on average about 25% of the offspring of two heterozygous carriers will be affected. Last, consanguinity is observed more often in pedigrees of autosomal-recessive disorders compared to autosomal-dominant conditions. Consanguinity refers to the mating of closely related individuals, who are more likely to share the identical disease-causing alleles of a locus because of descent from a common ancestor.

X-Linked Disorders

Genes that are located on the X or Y chromosome are known as sex-linked genes. The Y chromosome has relatively few genes and is the smallest of the human chromosomes, about 70 megabases (Mb). One important gene on the Y chromosome is called the sex-determining region Y (SRY) gene. Mutations of SRY can result in individuals with normal external female genitalia and gonadal dysgenesis (ie, abnormal formation of the gonads). However, this is an uncommon cause of abnormalities of sexual differentiation in humans.

The X chromosome is more than twice as large as the Y chromosome (about 160 Mb) and contains about 1000 genes that play a variety of roles during development and adult life. A number of well-known pediatric genetic conditions are caused by alterations of X-linked genes, including hemophilia A, Duchenne and Becker muscular dystrophies, red–green color blindness, ocular albinism with neurosensory hearing loss, anhidrotic ectodermal dysplasia, and ornithine transcarbamoylase deficiency. In addition, loci for more than 60 phenotypes associated with mental retardation (eg, fragile X syndrome) have been mapped to the X chromosome, although genes have been cloned for only a handful of these conditions.

Females have two copies and males one copy of the X chromosome. Yet the quantity of product encoded by most X-linked genes does not differ between males and females. The equalization of X-linked gene products is called dosage compensation and is produced by the inactivation of one of the X chromosomes early in female embryonic development. This inactivation process is random, so the maternally and paternally derived X chromosomes will each be inactive in about half of the embryo’s cells. Once an X chromosome is inactivated, the same X chromosome remains inactivated in all descendants of the cell. Thus, all normal females have at least two populations of cells (somatic mosaicism), one containing a paternally derived active X chromosome and the other containing a maternally derived active X chromosome, which becomes clearly evident if the maternally and paternally derived X chromosomes produce different products. For example, the retinas of women who are carriers for X-linked ocular albinism demonstrate alternating patches of pigmented and nonpigmented cells corresponding respectively to cells in which the disease-bearing X chromosome (nonpigmented) or the normal X chromosome (pigmented) has been inactivated.

Inactivation of the X chromosome takes place approximately 2 weeks after fertilization, begins in a region of the X chromosome called the inactivation center, and subsequently spreads along the chromosome. The X inactivation center contains at least one gene required for inactivation, XIST. XIST is transcribed only from the inactive X chromosome, but its mRNA never leaves the nucleus and is not translated into protein. The mRNA product of XIST appears to coat the portions of the X chromosome that are subsequently inactivated. Maintenance of inactivation appears to depend on methylation of CG dinucleotide repeats that are commonly found in the 5´ (upstream) regions of genes. Inactivation of the X chromosome is incomplete, and genes in several regions continue to be transcribed from the inactivated X chromosome. Some of these genes have transcribed homologues on the Y chromosome, and thus dosage compensation is maintained by their activation on both X chromosomes in females.

The inheritance patterns of X-linked conditions differ substantially from the inheritance patterns of autosomal disorders. Females can be homozygous for a disease allele at a given locus, heterozygous for a disease allele and a normal allele, or homozygous for a normal allele at a locus. Males have only one X chromosome and are considered hemizygous (hemi-, “half”) for an allele at a locus on the X chromosome. If a male inherits the altered allele for a recessive disorder, he will be affected with the condition because the Y chromosome does not carry a normal allele that might compensate for the effects of the disease gene. In contrast, X-linked dominant disorders can cause the disease condition in either males or females because the presence of only one copy of an altered allele is sufficient for disease expression.

For X-linked recessive disorders, the frequency of the disease condition in males is equal to the gene frequency q. This is because all males with the altered gene have the disease condition. Because females need two copies of the altered allele to manifest the condition, the frequency of the disease condition is q2. For example, hemophilia A has a prevalence of approximately 1/10,000 males (q = 0.0001). Thus, affected females will be observed in q2 (q2 = 0.00000001) or 1/100,000,000 individuals. Consequently, X-linked recessive disorders are likely to be found much more frequently in males than females.

A pedigree (Fig. 170-3) illustrates some of the important characteristics of an X-linked recessive trait. First, only females are able transmit the disorder to their sons; in other words, there is no male-to-male transmission for X-linked recessive conditions. Second, sibships containing only carrier females (unaffected) appear as “skipped generations.” In these generations, carrier females appear unaffected, and the X chromosome transmitted to males by their mother contains a normal allele. An affected father transmits the disease allele to all his daughters, who in turn transmit it to half of their sons on average.

At least three mechanisms account for some female carriers of X-linked recessive disorders manifesting some of or all the characteristics of the condition. First, because inactivation of the X chromosome is a random process within each cell, sometimes a much higher proportion of X chromosomes bearing a normal allele is inactivated than X chromosomes carrying a disease allele. These affected carrier females are known as manifesting heterozygotes. For many disorders, manifesting heterozygotes have a milder form of the condition compared with affected males. For example, approximately 5% of women carrying an allele for hemophilia A have factor VIII levels low enough to cause a mild form of the disease. Second, some women have only a single X chromosome (ie, Turner syndrome, see below) and therefore will manifest X-linked recessive conditions for which they would otherwise have been carriers. Last, chromosomal aberrations such as deletions or rearrangements involving the X chromosome and an autosome can also result in affected females. X chromosome rearrangements involving the mutation-containing X chromosome cause disease in females because the normal X chromosome will be preferentially inactivated to avoid inactivating the autosome attached to the other X chromosome. These events are relatively rare.

Some single-gene conditions are caused by mechanisms that are transmitted in patterns that are distinct from those of autosomal and sex-linked conditions. Many of these conditions are relatively uncommon. Nevertheless, these nontraditional mechanisms of disease often explain cases that are otherwise inconsistent with the current state of knowledge of genetic disorders. For example, the expression of most traits is independent of the parent of origin of the causative allele. Recently, however, it has become apparent that this is not always true. One of the most striking examples to date is caused by a deletion of 2 to 4 Mb of chromosome 15. When this deletion is inherited from the father, the offspring is born with Prader-Willi syndrome: severe neonatal hypotonia, obesity, small hands and feet, and an unusual behavioral profile including mental retardation (Fig. 170-4). In contrast, when the deletion is inherited from the mother, the offspring manifests Angelman syndrome, appearing normal at birth but subsequently developing seizures, mental retardation, ataxia, and a characteristic posture.

Within the 2 to 4 Mb region of chromosome 15 that is deleted in patients with either Prader-Willi or Angelman syndrome lie several genes that are transcriptionally active on one of the chromosomes inherited from the mother or father but not both (ie, they are active on only one chromosome). If these genes are deleted, the result is a complete loss of the encoded product and a disease condition. If all of the paternally active genes are lost, the offspring has Prader-Willi syndrome (Fig. 170-5). Angelman syndrome results from the deletion of a maternally active gene called ubiquitin-protein ligase E3A (UBE3A) that is involved in the degradation of proteins within the brain (Fig. 170-5). The differential activation of genes contingent on whether they are maternally or paternally transmitted is called genomic imprinting.

Approximately 70% of cases of Angelman or Prader-Willi syndrome are caused by chromosome deletions. However, several additional mechanisms may also cause these disorders. One of these is the inheritance of both copies of a chromosome, in part or the whole chromosome, from only one parent, called uniparental disomy. Thus, if both copies of the maternal chromosome 15 are inherited, the resulting offspring lacks the paternally active genes and develops Prader-Willi syndrome. Conversely, uniparental disomy of paternal chromosome 15 causes Angelman syndrome. Uniparental disomy also has been found to be responsible for some cases of Beckwith-Wiedemann syndrome. Uniparental disomy has been reported for most human chromosomes, although these abnormalities are, overall, uncommon.

Other cases that have been difficult to explain until recently include the expression of autosomal-recessive conditions (eg, cystic fibrosis) in the offspring of matings between a carrier parent (ie, heterozygous for a disease allele and a normal allele) and an unaffected parent homozygous for two normal alleles. Using molecular markers that can identify specifically each of the four parental chromosomes, it was found that both copies of the chromosome bearing a disease allele were identical and inherited from the heterozygous parent (uniparental isodisomy). The proportion of genetic conditions caused by this type of abnormality appears to be low.

The majority of genetic conditions are caused by abnormalities of the nuclear genome. Nevertheless, a growing number of conditions are caused by defects of the only genetic material existing outside of the nucleus, that of the mitochondria. In contrast to the nuclear genome, which is diploid (two copies of each gene), the mitochondrial genome contains only one copy of each gene and is thus haploid. Because of the unique properties of mitochondria, these disorders exhibit a characteristic pattern of inheritance and wide phenotypic variability. Each of the 100 to 100,000 mitochondria within a cell contains at least several copies of a 16,569-bp genome in the mitochondrial matrix, and each mitochondrial DNA (mtDNA) molecule is identical. The state in which all copies of mtDNA are identical is called homoplasmy. The mtDNA molecule encodes 13 polypeptides that are components of the oxidative phosphorylation (OXPHOS) system (another approximately 90 components are encoded by the nuclear genome), 2 ribosomal RNAs, and 22 transfer RNAs. Replication and transcription of mtDNA take place within the mitochondria and are facilitated by nuclear-encoded proteins. In humans, mitochondria in the midpiece of the sperm may enter the egg, but the mtDNA from the sperm rarely, if ever, persists in the embryo. Thus all the mitochondria of the offspring are descendants of those located within the cytoplasm of the egg. Consequently, the inheritance of mtDNA is exclusively maternal.

Because there is more than one copy of mtDNA within each mitochondrion, a new mutation in an mtDNA molecule will result in the emergence of two different mtDNA populations within a mitochondrion. The state of having two or more different populations of mtDNA molecules is called heteroplasmy. As cells divide and the mitochondria proliferate, the proportion of mutant mtDNA molecules within a cell and the proportion of cells in a tissue or organ containing mitochondria with mutant mtDNA molecules will change. Mutant mtDNAs diminish the efficiency of OXPHOS metabolism and cause cells to die and tissues and organs to deteriorate prematurely. A threshold of mutant mtDNA molecules within a mitochondrion (typically 85%) must be exceeded before a biochemical defect disrupts the normal function of the OXPHOS system. Thus, the larger the proportion of mutant mtDNA molecules within a cell or tissue is, the higher will be the likelihood of expressing a disease phenotype or the greater the severity of disease.

Mitochondrial disorders are commonly classified according to the type of mutation that causes them or their clinical presentation (Table 170-1). In general, mutations in the mtDNA molecule are either rearrangements (ie, deletions and duplications) or point mutations (ie, missense or nonsense mutations). Many mtDNA disorders present with nonspecific neurologic findings such as coma, seizures, and ataxia. In the neonatal period, mitochondrial disorders commonly present with metabolic encephalopathy, cardiac or hepatic failure, and/or lactic acidemia. Although uncommon, mitochondrial disorders account for a substantial percentage of cerebrovascular accidents in children. Most mitochondrial disorders are uncommon, but mtDNA mutations also contribute to common disorders such as deafness and diabetes mellitus. Mitochondrial mutations have also been implicated in the process of aging. However, whether these mutations are a cause or a consequence of the aging process is unclear.

The identification and characterization of a disease gene are the first steps in understanding the molecular pathogenesis of a condition. Further insight is often gained by understanding the mechanism by which mutations disturb the function of a cell. Most mutations result in either a gain of function or loss of function of the encoded product.

A disease allele occasionally results in a protein product with a novel function compared to the normal product. More commonly a disease allele causes the overexpression of its product or expression of its product at an inappropriate time or place. These types of mutations are known as gain-of-function mutations and commonly result in conditions transmitted in a dominant pattern. Huntington disease, a late-onset condition characterized by progressive neurologic deterioration, is caused, in part, by a gain-of-function mutation.

Some gain-of-function mutations extend the normal function of a gene. For example, mutations in fibroblast growth factor 3, FGFR3, result in the uncontrolled activation of the receptor leading to enhanced inhibition of the growth of long bones (eg, the femur). Depending on the location of the mutation, this produces hypochondroplasia, achondroplasia, or thanatophoric dysplasia.

Some mutations result in the loss of 50% of the encoded product, and 50% of the product remains available (encoded by the normal allele). Often, but not exclusively, these loss-of-function mutations are observed in recessive conditions (eg, galactosemia, Hurler syndrome). Since carriers for most recessive disorders are asymptomatic, the availability of 50% of the encoded product is often enough to prevent disease. In circumstances in which 50% of the encoded product is not sufficient to prevent disease (haploinsufficiency), a loss-of-function mutation can also result in dominant disorders. For example, a deletion of the gene encoding the extracellular matrix protein, elastin, results in diminished incorporation of elastin into the wall of large arteries, producing supravalvular aortic stenosis.

Another type of loss-of-function mutation results when the encoded product is not only nonfunctional, but also interferes with the activity of the normal product and is known as dominant negative mutation. This type of mutation is usually observed in genes that encode proteins that are components of multimeric (containing two or more protein subunits) proteins. For example, mutations in one of the collagen genes (COL1A1) can impair the binding of collagen subunits into a normal trimeric complex, resulting in osteogenesis imperfecta.

Over the last decade a novel type of mutation produced by an expansion of a repeated nucleotide motif has been found to cause a variety of genetic conditions. Most commonly, these disorders are associated with an expansion of a trinucleotide repeat (eg, CAG, CTG). These repeats can be located within a gene or in the 5′ or 3′ untranslated portions of a gene. One of the most notable of the genetic conditions caused by an expansion of a trinucleotide repeat is fragile X syndrome, the most common cause of inherited mental retardation in males.

Fragile X syndrome is an X-linked condition with 80% penetrance in males and 30% penetrance in females. It is caused by the expansion of a CGG repeat in the 5′ untranslated region of a gene called FMR1. In unaffected men, there are typically 6 to 50 CGG repeats. Males who carry the disease allele but do not have fragile X syndrome are called transmitting males. An intermediate number of repeats (ie, 50–230), or premutation, is found in transmitting males and their female offspring. When these female offspring transmit the gene to their offspring, the premutation expands to a full mutation ranging up to several thousand repeats. Men with full mutations have no FMR1 mRNA in their cells, indicating that transcription of FMR1 has been silenced. Furthermore, premutations tend to become larger in successive generations, and larger premutations are more prone to expansion to a full mutation. These expansions do not occur when a male transmits the premutation. This explains why males with a premutation cannot transmit the disease to their daughters and why grandsons and great-grandsons of normal transmitting males are more likely to be affected with fragile X syndrome.

Expansions of trinucleotide repeats are also associated with various progressive neurodegenerative disorders, including some of the spinocerebellar ataxias, Huntington disease, and myotonic dystrophy. As discussed previously, some of these trinucleotide repeat expansions are also associated with anticipation. The expansion of a 12-bp repeat from 2 or 3 repeats to approximately 60 repeats has been discovered to cause autosomal-recessive myoclonic epilepsy.

The prevalence of many genetic disorders varies extensively among human populations. For example, the prevalence of cystic fibrosis varies from 1/313 in the Hutterites of Alberta, Canada, to 1/90,000 in Asians, a difference of nearly 300-fold. Although mutation is ultimately the source of all variation in the genome, different mutation rates among populations are not a sufficient explanation for wide variation in prevalence rates of genetic conditions. Varied prevalence rates are the imprints left by evolutionary forces other than mutation (ie, natural selection, genetic drift, gene flow) on disease-related variation in human populations. Explaining these patterns of disease-related genetic variation facilitates understanding the etiology and pathogenesis of genetic conditions. However, estimating disease-related genetic variation depends on understanding the distribution of total genetic variation. Over the past decade a variety of new molecular and statistical tools for estimating genetic variation have been applied widely to human populations to further explain the genetic bases of various medical conditions and traits. Further, these tools have provided new insights about how evolutionary forces have shaped disease-related genetic variation in contemporary populations.

Genetic drift refers to the random fluctuations in gene frequencies that occur from generation to generation as the result of sampling a limited number of gametes. As the size of the population decreases, the degree of fluctuation increases. Genes that are rare in large populations may be common in small populations or vice versa. Genetic drift can be caused by a substantial reduction in the size of a population (a population bottleneck) or the separation of a subset of a larger population (founder effect). For example, according to well-maintained historical records, the Old Order Amish in Lancaster County, Pennsylvania, were established by approximately 50 couples. Nearly half of all the reported cases of Ellis-van Creveld (EVC) syndrome (an autosomal-recessive skeletal dysplasia characterized by short stature, polydactyly, and cardiac defects caused by mutations in EVC) have been identified in the Amish population. The relatively small founding population of the Amish and their custom of marrying only within their relatively isolated community (endogamy) have resulted in a very high carrier frequency of the disease-causing alleles of EVC.

Natural selection alters the frequency of a trait (disease condition) contingent on the relative fitness of a phenotype in a given environmental context. Phenotypes with a high fitness are positively selected, and phenotypes with a low fitness are negatively selected. Traditionally, fitness has been estimated by the number of descendants produced by those who possess a given genotype or phenotype. For example, individuals who die without descendants have a fitness of zero, whereas individuals with higher numbers of offspring have higher fitness values. Diseases maintained in a population by natural selection illustrate the relationship among genes, phenotypes, and the environment. Consanguinity is defined as the mating of related individuals. Although consanguinity is relatively rare in Western populations, it is common in many populations of the world. Consanguinity increases the chances that a mating couple will both carry the same disease allele. Thus, consanguineous matings are more likely to produce offspring affected with autosomal-recessive disorders.

Many studies have shown that mortality rates among the offspring of first-cousin marriages are substantially higher than in the general population. Furthermore, the prevalence of genetic disease is approximately twice as high among the offspring of first-cousin marriages. There are few data about the mating of first-degree relatives (ie, incestuous matings), although the prevalence of mental retardation, short stature, and major congenital anomalies is clearly higher.