Alleles Explained: Different Versions of the Same Gene

An allele is one of the different versions of a gene. Alleles occupy the same position, or locus, on corresponding chromosomes, but their DNA sequences can differ.

That difference can be tiny—sometimes just a single DNA base—or involve a larger change in the sequence. Alleles are one reason people can have different traits, such as blood types or certain inherited characteristics, even though humans share most of the same genes.

Understanding alleles also helps explain inheritance, dominant and recessive traits, genetic variation, and why a person can carry a genetic variant without showing its associated trait.

What is a gene?

A gene is a segment of DNA that contains information used by cells to make a functional product, usually a protein or, in some cases, a functional RNA molecule. Genes contribute to the biological instructions that help cells develop, function, and respond to their surroundings.

Most human body cells contain chromosomes in pairs. One chromosome in each pair was inherited from the biological mother and the other from the biological father. The corresponding chromosomes contain many of the same genes in the same general locations.

However, the DNA sequence of a particular gene can vary between people. These alternative forms are alleles.

For example, imagine a gene at a particular chromosome location that has two common DNA versions. One person might inherit one version from each parent, while another person might inherit two different versions. The gene is the same gene in both people, but the alleles they carry differ.

What makes one allele different from another?

Alleles differ because their DNA sequences are not identical. A difference can arise through a mutation, meaning a change in DNA sequence. If such a change occurs in a cell lineage that can contribute to reproduction, it may be passed to future generations.

Some DNA differences have little or no detectable effect on a person’s biology. Others can alter how much of a gene product is made, change the structure or function of a protein, or affect how a gene is regulated.

An allele therefore should not automatically be thought of as a “good” or “bad” version of a gene. Its biological effect depends on the gene, the particular DNA change, the person’s other alleles, and sometimes environmental factors.

How do people inherit alleles?

For most genes located on the autosomal chromosomes—the chromosomes other than X and Y—people generally inherit one allele from each biological parent.

This gives an individual two copies of most autosomal genes. The two alleles may be identical or different.

If the two alleles are the same, the person is homozygous at that gene. If the alleles differ, the person is heterozygous.

Consider a simplified example in which a gene has two alleles, A and a:

These symbols are simply a convenient way to represent alleles. Real genes are made of DNA sequences, not single letters such as A or a.

During the formation of eggs and sperm, chromosome pairs separate so that each reproductive cell typically receives one chromosome from each pair. When an egg and sperm combine at fertilization, the resulting individual receives one allele from each parent for most autosomal genes.

Alleles and dominant and recessive inheritance

One of the most familiar ways alleles differ is through dominant and recessive inheritance.

A dominant allele can contribute to a trait when only one copy is present. A recessive allele generally produces its associated phenotype only when a person has two copies, in the simplified inheritance patterns commonly taught in introductory genetics.

For instance, if A is dominant and a is recessive:

• AA shows the dominant phenotype.
• Aa also shows the dominant phenotype.
• aa shows the recessive phenotype.

This does not mean that the dominant allele is stronger, healthier, or more common. “Dominant” describes a pattern of expression in a particular genetic context.

Likewise, a recessive allele is not necessarily rare or harmful. Dominant and recessive are terms describing relationships between alleles and their effects on a phenotype.

Many real biological traits are more complicated than the simple dominant-recessive model. A gene can have multiple alleles, alleles can show codominance or incomplete dominance, and traits can be influenced by many genes and environmental factors.

What is a genotype?

A person’s genotype refers to the genetic information they carry. When discussing a particular gene, genotype can describe the combination of alleles at that gene.

A person’s phenotype is the observable characteristic or measurable biological property resulting from genetic and environmental influences.

The distinction matters because knowing someone’s genotype does not always tell you exactly what their phenotype will be. Some genetic effects depend on other genes, developmental conditions, environment, or whether a particular allele is expressed.

For example, two people can carry different alleles yet have the same observable trait. Conversely, a genetic difference can contribute to a trait without being the sole cause of it.

Can a gene have more than two alleles?

Yes. A population can contain many different alleles of the same gene.

An individual, however, generally carries no more than two alleles of an autosomal gene because they have two copies of each autosomal chromosome. A population can contain many alleles even though each person carries only a subset of them.

A classic example is the ABO blood group system, in which three common alleles—often designated Iᴬ, Iᴮ, and i—contribute to the familiar A, B, AB, and O blood-group phenotypes. Iᴬ and Iᴮ are codominant with each other, while i is recessive to both.

This illustrates why “a gene has two alleles” is an oversimplification. Two alleles may be used in a particular example, but a gene can have numerous allelic forms in a population.

Are alleles the same as genetic variants?

The terms are closely related but are not always interchangeable.

A genetic variant is a difference in DNA sequence compared with another sequence or reference. An allele is a particular version of a genetic sequence at a defined location.

In everyday genetics, the distinction can be subtle because a variant can define an allele. The word “variant” is often preferred when discussing DNA differences without implying that the difference has a particular effect on health or traits.

Importantly, not every genetic variant causes disease. Human genomes naturally contain many differences, and most do not have a harmful effect.

How alleles contribute to genetic diversity

Alleles are a fundamental source of genetic variation within populations. Differences in DNA accumulate through processes such as mutation and can be passed through generations.

Natural selection can affect how frequently particular alleles occur when differences influence survival or reproductive success. Other evolutionary processes, including genetic drift and migration between populations, can also change allele frequencies.

This means that an allele’s frequency in a population can change over time. An allele can be common without being dominant, and an allele can be rare without being recessive. Dominance and population frequency are different concepts.

What about genes on the X and Y chromosomes?

The basic “one allele from each parent” model needs modification for genes on the sex chromosomes.

People with two X chromosomes generally have two copies of genes located on the X chromosome, although X-chromosome biology involves additional mechanisms such as X-inactivation. People with one X chromosome and one Y chromosome generally have only one copy of many X-linked genes.

As a result, an individual with only one copy of a particular X-linked gene does not have a second allele at that locus to interact with the first in the usual way. This helps explain distinctive inheritance patterns for some X-linked genetic conditions.

Genes located on the Y chromosome have their own inheritance pattern because the Y chromosome is transmitted through the paternal line in typical human reproduction.

Why alleles matter in health and medicine

Alleles can influence susceptibility to genetic disorders, responses to medications, physical characteristics, and many other biological traits.

Some conditions result primarily from changes in a single gene. In such cases, knowing which allele or alleles a person carries can be important for diagnosis, inheritance counseling, or assessing the likelihood of developing a condition.

Other conditions are multifactorial, meaning that many genetic variants interact with one another and with environmental influences. In these situations, there usually is no single allele that determines the outcome.

It is also important to distinguish between carrying an allele and having a disease. A person may carry a disease-associated allele without developing the condition, depending on the inheritance pattern, the allele’s effect, other genetic factors, and the particular disorder.

The key idea

An allele is simply a specific version of a gene. Most people have two alleles for each autosomal gene—one inherited from each biological parent—and those alleles may be the same or different.

The differences between alleles help create genetic variation. Their effects can range from essentially none to substantial biological consequences, and the way those effects are inherited can be simple or highly complex.

Once the distinction between gene and allele is clear, many basic genetics concepts fall into place: genes are stretches of genetic information, while alleles are the different versions of those genes that individuals and populations carry.