# Sex linkage

Sex linkage describes the sex-specific patterns of inheritance and expression when a gene is present on a sex chromosome (allosome) rather than a non-sex chromosome (autosome). Genes situated on the X-chromosome are thus termed X-linked, and are transmitted by both males and females, while genes situated on the Y-chromosome are termed Y-linked, and are transmitted by males only. As human females possess two X-chromosomes and human males possess one X-chromosome and one Y-chromosome, the phenotype of a sex-linked trait can differ between males and females due to the differential number of alleles (polymorphisms) possessed for a given gene. In humans, sex-linked patterns of inheritance are termed X-linked recessive, X-linked dominant and Y-linked. The inheritance and presentation of all three differ depending on the sex of both the parent and the child. This makes sex-linked patterns of inheritance characteristically different from autosomal dominance and recessiveness. This article will discuss each of these patterns of inheritance, as well as diseases that commonly arise through these sex-linked patterns of inheritance.

## Background on Sex Determination and Human Sex Chromosomes

In humans (and mammals in general), biological sex is determined by genetics; however this is not the case for all animals, for instance, the biological sex of some reptiles is environmentally determined, and the sex of some worms is dependent on location.
Sex chromosomes and how they interact with Mendelian inheritance were discovered by Nettie Stevens. Stevens found that biological females carry two X chromosomes and males carry one X, and was the first to determine that they also carried a small Y chromosome. With the identification of the Y chromosome, Stevens was able to link its presence with male development.
22 of the 23 pairs of human chromosomes are autosomal (not involved in sex determination), while the 23rd pair of human chromosomes are the sex chromosomes. The possession of two X-chromosomes defines a biological female, while the possession of one X and one Y chromosome defines a biological male. The two sex chromosomes differ in size and gene content, and unlike the sets of autosomal chromosomes, are not homologous. The X-chromosome contains an estimated 1400 genes, most of which are involved in tissue development and the development of human disorders. The Y-chromosome is host to the SRY gene, which is involved in the development of several male sex characteristics, while the identified functions of many of the remaining approximately 200 genes on the Y-chromosome are associated with human disease. Sex linkage thus refers to the association of a trait encoded by one of the genes on these sex chromosomes. There are many more X-linked conditions than Y-linked conditions due to the larger size of the X-chromosome and greater number of genes encoded within it.

## Sex linked Patterns of Inheritance

A disease or trait determined by a gene on the X chromosome demonstrates X-linked inheritance, which can be divided into dominant and recessive patterns.
In X-linked recessive inheritance, a son born to a carrier mother and an unaffected father has a 50% chance of being affected, while a daughter has a 50% chance of being a carrier, however a fraction of carriers may display a milder (or even full) form of the condition due to a phenomenon known as skewed X-inactivation, in which the normal process of inactivating half of the female body's X chromosomes preferably targets a certain parent's X chromosome (the father's in this case). If the father is affected, the son will not be affected, as he does not inherit the father's X chromosome, but the daughter will always be a carrier (and may occasionally present with symptoms due to aforementioned skewed X-inactivation).
In X-linked dominant inheritance, a son or daughter born to an affected mother and an unaffected father both have a 50% chance of being affected (though a few X-linked dominant conditions are embryonic lethal for the son, making them appear to only occur in females). If the father is affected, the son will always be unaffected, but the daughter will always be affected. A Y-linked condition will only be inherited from father to son and will always affect every generation.
In classical genetics, a mating experiment called a reciprocal cross is performed to test if an animal's trait is sex-linked.
| (A) | (B) | (C) |
* Illustration of some X-linked heredity outcomes (A) the affected father has one X-linked dominant allele, the mother is homozygous for the recessive allele: only daughters (all) will be affected. (B) the affected mother is heterozygous with one copy of the X-linked dominant allele: both daughters and sons will have 50% probability to be affected. (C) the heterozygous mother is called "carrier" because she has one copy of the recessive allele: sons will have 50% probability to be affected, 50% of unaffected daughters will become carriers like their mother.

## X-linked Dominant Inheritance

X-linked dominant inheritance, sometimes referred to as X-linked dominance, is a mode of genetic inheritance by which a dominant gene is carried on the X chromosome. As an inheritance pattern, it is less common than the X-linked recessive type. In medicine, X-linked dominant inheritance indicates that a gene responsible for a genetic disorder is located on the X chromosome, and only one copy of the allele is sufficient to cause the disorder when inherited from a parent who has the disorder. In this case, someone who expresses an X-linked dominant allele will exhibit the disorder and be considered affected. The pattern of inheritance is sometimes called criss-cross inheritance.
X-linked dominant traits do not necessarily affect males more than females (unlike X-linked recessive traits). The exact pattern of inheritance varies, depending on whether the father or the mother carries the allele for the trait of interest. All daughters of a father affected by an X-linked dominant disorder will have also be affected, as they receive their father's only X-chromosome. Sons of a father affected by an X-linked dominant disorder will not be affected, as they receive the father's unaffected Y-chromosome. Both daughters and sons born to a mother heterozygous for an X-linked dominant trait will have a 50% chance of being affected, depending on which X-chromosome they receive from the mother. However, a son affected by an X-linked dominant trait will always have an affected mother. Some X-linked dominant conditions are embryonic lethal in males, making them appear to only occur in females.

### Frequency and Patterns of Inheritance

In X-linked dominant inheritance, when the mother alone is the carrier of a mutated, or defective gene associated with a disease or disorder; she herself will have the disorder. Her children will inherit the disorder as follows:
* Of her daughters and sons: 50% will have the disorder, 50% will be completely unaffected. Children of either sex have an even chance of receiving either of their mother's two X chromosomes, one of which contains the defective gene in question.
When the father alone is the carrier of a defective gene associated with a disease or disorder, he too will have the disorder. His children will inherit the disorder as follows:
* Of his daughters: 100% will have the disorder, since all of his daughters will receive one copy of his single X chromosome.
* Of his sons: none will have the disorder; sons do not receive an X chromosome from their father.
If both parents were carriers of a defective gene associated with a disease or disorder, they would both have the disorder. Their children would inherit the disorder as follows:
* Of their daughters: 100% will have the disorder, since all of the daughters will receive a copy of their father's X chromosome.
* Of the sons: 50% will have the disorder, 50% will be completely unaffected. Sons have an equal chance of receiving either of their mother's X chromosomes.
In such a case, where both parents carry and thus are affected by an X-linked dominant disorder, the chance of a daughter receiving two copies of the X chromosome with the defective gene is 50%, since daughters receive one copy of the X chromosome from both parents. Were this to occur with an X-linked dominant disorder, that daughter would likely experience a more severe form.
Some X-linked dominant conditions such as Aicardi syndrome are fatal to boys; therefore only girls with these conditions survive, or boys with Klinefelter's syndrome (and hence have more than one X chromosome).
A few scholars have suggested discontinuing the use of the terms dominant and recessive when referring to X-linked inheritance, stating that the highly variable penetrance of X-linked traits in females as a result of mechanisms such as skewed X-inactivation or somatic mosaicism is difficult to reconcile with standard definitions of dominance and recessiveness.

## X-linked Recessive Inheritance

X-linked recessive inheritance describes one of the patterns of inheritance of genetic traits or disorders encoded by an allele (version of a gene) situated on the X-chromosome. In X-linked recessive inheritance, females (XX) must have two copies of the allele (homozygous), while males (XY) require only one copy of the allele (hemizygous) to display the phenotype. Thus, it is far more common for males to be affected by X-linked recessive traits.
A female heterozygous for an X-linked recessive trait is considered a carrier. While a carrier female most often does not display the phenotype, rare cases of skewed X-chromosome inactivation can lead to varied levels of expression.
There are characteristic patterns for X-linked recessive inheritance. As each parent contributes one sex chromosome to their offspring, sons cannot receive the X-linked trait from affected fathers, who provide only a Y-chromosome. Consequently, affected males must inherit the X-linked recessive trait from their mothers. Sons of a healthy carrier female have a 50% change of being affected, while sons of an affected female will always be affected. Females must inherit a X-linked recessive allele from each parent. All daughters of an affected father and healthy non-carrier mother will be carriers. Daughters of an affected father and carrier mother will have a 50% chance of being affected, and daughters of two affected parents will always be affected. While there is no male-to-male transmission of X-linked recessive traits, an affected male can pass his recessive X allele to a grandson through his unaffected carrier daughter.

## X-linked Diseases
### X-linked Dominant diseases

* Aicardi Syndrome
* Alport syndrome (majority of cases)
* Coffin–Lowry syndrome (CLS)
* Fragile-X Syndrome
* Giuffrè–Tsukahara syndrome
* Goltz syndrome
* Idiopathic hypoparathyroidism
* Incontinentia pigmenti
* Porphyria (2-10% of cases)
* Rett syndrome (5% of cases)
* Vitamin D resistant rickets (X-linked hypophosphatemia)

### X-linked Recessive Diseases

The incidence of X-linked recessive conditions in females is the square of that in males: for example, if 1 in 20 males in a human population are red–green color blind, then 1 in 400 females in the population are expected to be color-blind ($^1$/$_{20}$)*($^1$/$_{20}$). Examples include:
* Aarskog–Scott syndrome
* Adrenoleukodystrophy (ALD)
* Bruton's agammaglobulinemia
* Color blindness
* Complete androgen insensitivity syndrome
* Congenital aqueductal stenosis (hydrocephalus)
* Duchenne muscular dystrophy
* Fabry disease
* Glucose-6-phosphate dehydrogenase deficiency
* Haemophilia A and B
* Hunter syndrome
* Inherited nephrogenic diabetes insipidus
* Menkes disease (kinky hair syndrome)
* Ornithine carbamoyltransferase deficiency
* Wiskott–Aldrich syndrome

#### Duchenne Muscular Dystrophy

Duchenne Muscular Dystrophy (DMD) is a severe neuromuscular disease causing progressive weakness and damage of muscle tissues, leading to mobility loss and difficulties in daily activities. In a later stage of DMD, as respiratory and cardiac muscles start to degenerate, affected individuals are likely to develop complications such as respiratory failure, cardiomyopathy and heart failure.
DMD arises from a mutation, likely to be the deletion of the exons, a nucleotide sequence in the DMD gene that codes for dystrophin. Dystrophin is a protein responsible for strengthening and stabilizing muscle fibres. With the loss of the dystrophin complex, the muscle cells would no longer be protected and therefore result in progressive damage or degeneration.

#### X-linked agammaglobulinemia

X-linked agammaglobulinemia (XLA) is a primary immunodeficiency disorder that impairs the body’s ability to produce antibodies, which are proteins protecting us from disease-causing antigens, resulting in severe bacterial infections.
XLA is associated with a mutation in the Bruton's tyrosine kinase (BTK) gene on the X chromosome, which is responsible for producing BTK, an enzyme regulating B cells development. B cells are a type of white blood cells essential in the production of antibodies, when at an early stage, called pre-B cells, they rely on expansion and survival signals involving BTK to mature.
In affected individuals, their BTK genes have an amino acid substitution mutation, altering the amino acid sequence and the structure of BTK making it faulty. Therefore, they have a normal pre-B cell counts but cannot develop mature B cells, resulting in antibody deficiency.

#### Red-green colour blindness

Red-green colour blindness is a type of colour vision deficiency (CVD) caused by a mutation in X-linked genes, affecting cone cells responsible for absorbing red or green light.
The perception of red and green light is attributed to the Long (L) wavelength cones and Medium (M) wavelength cones respectively. In Red-green colour blindness, mutations take place on the OPN1LW and OPN1MW genes coding for the photopigments in the cones. In milder cases, those affected exhibit reduced sensitivity to red or green light, as a result of hybridisation of the genes, shifting the response of one cone towards that of the other. In the more extreme conditions, there is a deletion or replacement of the respective coding genes, resulting in the absence of L or M cones photopigments and thus losing the ability to differentiate between red or green light completely.

#### Haemophilia A

Haemophilia A is a blood clotting disease caused by a genetic defect in clotting factor VIII. It causes significant susceptibility to both internal and external bleeding. Individuals having more severe haemophilia can experience more frequent and intense bleeding.
Severe haemophilia A affects most patients. Patients with mild haemophilia often do not experience heavy bleeding except for surgeries and significant trauma.
vteX-linked disorders :

## Screening for Genetic diseases

Genetic screening, which includes carrier screening, prenatal screening and newborn screening may be performed to enable early detection of genetic defects.

### Carrier screening

Carrier screening is conducted on prospective parent(s) to determine if they are carriers (heterozygous) for an X-linked recessive or autosomal recessive disease. Individuals who undergo carrier screening commonly have a family history of genetic disease or belong to an at-risk population and wish to determine the likelihood of having a child with a genetic disorder. Carrier screening is performed by taking a blood sample, saliva sample or buccal swab and using laboratory techniques such as next-generation sequencing or Polymerase Chain Reaction (PCR) to determine if the parent carries the allele implicated in the genetic disease.

### Prenatal screening

Prenatal screening is can be conducted on pregnant females to test for a number of genetic conditions. It is more commonly used to test for aneuploidy (for example, Down syndrome or trisomy 21), but can also be used to detect X-linked recessive or X-linked dominant disorders (for example, fragile X-syndrome). Prenatal screening involves maternal blood tests and ultrasound to defect such defects in the developing fetus. This can confirm the diagnosis of a genetic condition, allowing parents to prepare or consider terminating the pregnancy.

### Newborn screening

Newborn screening is conducted on infants less than a week old to test for a variety of genetic disorders, specifically those with high morbidity and mortality rates to enable early intervention. Newborn screening is conducted by analyzing the biochemistry of a spot of dried blood (often obtained via a heel prick test). This form of screening is also used to detect endocrine and metabolic disorders.

## Y-linked Inheritance
### The Y chromosome

The Y chromosome is comprised of approximately 59 million base pairs and 200 genes, entailing approximately 66 protein-coding genes. Since only biological males possess the Y chromosome, it is essential in male sexual differentiation, which results in the production of male sex hormones that lead to the development of male sex organs, reproduction, fertility, and spermatogenesis, commonly known as sperm production. Additionally, due to the small length of the Y chromosome in comparison to the X chromosome, recombination is mostly suppressed, and thus it remains relatively distinct from the X chromosome, maintaining important genes for male fertility and sexual differentiation. Particularly, the SRY gene on the Y chromosome is known to be involved in sex determination.
The Y chromosome has a highly repetitive sequence, and thus had many gaps that were not able to be sequenced until recently. Based on advances in the Makova Lab at Penn State and Phillippy at the Human Genome Research Institute, they successfully filled in the missing sequence gaps.

### The SRY gene

The SRY gene, being the sex-determining region of the Y chromosome, gives the genetic information required for the body to code for proteins that are involved in male sexual differentiation. The expression of the SRY gene is regulated via a myriad of transcription factors, which is a protein that can bind to genes of interest and increase or decrease their expression. Specific to SRY these include, Six1, WT1, and Gata4. SRY expression is regulated spatially and temporally in a strict manner. The SRY gene encodes a transcription factor called the the Testes Determining Factor (Tdf), and Tdf binds to activates another gene called Sox9. Sox9 then codes a transcription factor that leads to the development of the testes via many downstream pathways that ultimately result in the targeting of Sertoli cell which is where sperm is produced and the Lydig cell, also called testicular somatic cells, which is where the androgen hormone is produced, that is essential for male sexual differentiation. Therefore, SRY expression leads to testis development in biology XY males, and absence of SRY in biological XX females, leads to ovary development.
Swyer syndrome, also known as complete gonadal dysgenesis or pure gonadal dysgenesis, is a condition that impairs the process of sexual differentiation in males. Male individuals with this condition have a normal XY genotype, yet due to the impairment of the SRY gene, the protein critical in male sexual determination is non-functional or is not produced at all. As a result, male sexual differentiation is prevented, and an affected individual will lack male sexual characteristics such as gonads, and will instead develop biological female-typical sex characteristics, such as a uterus, fallopian tubes, etc..

### Y-linked Inheritance

Y-linked inheritance, also known as Holandric inheritance, refers to genes that are inherited via the Y chromosome. In other words, Y-linked inheritance involves genes that are only carried on the Y chromosome, also known as Y-linked genes.
Inheritance of Y-linked genes can occur in two ways: complete inheritance and incomplete inheritance. Complete Y-linkage results when a gene is only found on a certain area on the Y chromosome either because there is no allele i.e. a copy of that gene, on the X chromosome or because it does not exchange with the X chromosome's allele. Complete Y linkage of heterogamous organisms can result in the following possible outcomes:
* Traits that only occur in males
* Y-linked disorders of males will be passed on to all sons
* The daughters of affected men being phenotypically normal, i.e. 'normal' presenting, and not having affected offspring
Conversely, incomplete Y linkage is when traits on a gene cross-over and exchange information between the X and Y chromosome.

### Y-linked Disorders:
#### Hypertrichosis:

Hypertrichosis is a genetic condition that results in the excessive growth of hair on a specific area of the body, that is abnormal for the age, sex or race of an individual. Specifically, hypertrichosis centralized to the outer ear, also known as the auricle, referred to as hypertrichosis pinnae auris, is a Y-linked disorder. Since hypertrichosis pinnae auris is a Y-linked disorder, this means only biological men and subsequent male offspring can be affected by this disorder. Tommasi C. was critical in determining the Y-linked origin of this disorder, by creating a pedigree that elicited holandric inheritance. Conversely, hypertrichosis cannot be confused with Hirustism, which is characterized by excessive androgen sensitive hair growth, and thus is most often diagnosed in women and children that tend to have male-typical hair patterns.

#### Webbed Toes:

Webbing of the toes is the result of premature arrested development in fetal stage. The premature arrest of development results in second and third digit fusion via the skin. The Y-linked trait of webbed toes causes a skin connection between the second and third digit. Research studies based in a pedigree analysis have shown that webbed toes follow holandric inheritance in biological males.

#### Infertility and hypo-fertility in males:
##### Overview:

Y-linked genes responsible for spermatogenesis can result in male infertility, characterized by azoospermia, or hypo-fertility, which is the hindered production of sperm. Azoospermia is the absence of functional sperm in male ejaculate due to issues in sperm motility or lack of sperm production. As a result, Y-chromosome infertility is also characterized as the inability to fertilize an egg and produce children. Sperm infertility results from the failure of the sperm to mature or a disfigured sperm that is not able to travel and fertilize an egg effectively.

##### Prevalence of Y chromosome Infertility:

Y chromosome infertility is relatively rare at a 0.03-0.05% frequency.

##### Etiology of Y chromosome Infertility:

Mutations to the MSY region most typically are the cause of spermatogenic failure, which is the reduced or absent sperm production in semen.

## Sex-linkage in Non-Human Animals

* The first sex-linked gene ever discovered was the "lacticolor" X-linked recessive gene in the moth Abraxas grossulariata by Leonard Doncaster.
* White eyes in Drosophila melanogaster flies was one of the earliest sex-linked genes discovered.
* Fur color in domestic cats: Calico or tortoiseshell cats are nearly always female because these cats receive one allele for black (or gray) fur colour on one inherited X-chromosome, and one allele for orange fur colour on the other X-chromosome. White fur colour is located on an autosome. Thus, only females and XXY males can have this fur coloration.
Patterns of inheritance differ in animals that use sex-determination systems other than XY. In the ZW sex-determination system used by birds, the mammalian pattern is reversed, since the male is the homogametic (ZZ) and the female is heterogametic (ZW).

## Related terms

It is important to distinguish between sex-linked characters, which are controlled by genes on sex chromosomes, and two other categories.

### Sex-influenced traits

Sex-influenced or sex-conditioned traits are phenotypes affected by whether they appear in a male or female body. Even in a homozygous dominant or recessive female the condition may not be expressed fully. Example: baldness in humans.

### Sex-limited traits

These are characters only expressed in one sex. They may be caused by genes on either autosomal or sex chromosomes. Examples: female sterility in Drosophila; and many polymorphic characters in insects, especially in relation to mimicry. Closely linked genes on autosomes called "supergenes" are often responsible for the latter.

## History

Red-green colour blindness was the first X-linked genetic disorder described on paper, in 1794 by John Dalton, who was affected by the disorder himself. However, it was not until later that the inheritance pattern and genetics were worked out. The X-chromosome was discovered in 1890 by Hermann Henking, then in 1910, Thomas Hunt Morgan discovered an X-linked mutation on a Drosophila, who then conducted experiments and observations to understand the X-linked inheritance.
In 1961, Mary Lyon proposed that one of the two X chromosomes in female mammalian cells would experience random inactivation (see X-chromosome inactivation) in the early embryonic stage. According to her hypothesis, both males and females should have one single X chromosome that is active. This enhanced the understanding of the fundamental mechanisms of X-linked inheritance.