What’s the Difference Between Genes and Alleles?
Updated on March 18, 2024
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What’s the Difference Between Genes and Alleles?
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Key Takeaways

What's the Difference Between Genes and Alleles? 1

Genes are the building blocks of your DNA, while alleles are the term for variants of a gene. Just like how the term “soda” refers to the carbonated beverage, soda can come in different flavors or brands.

What alleles (versions of a gene) you have in your DNA determines the majority of your physical traits. Read on to see how this works.

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What is an Allele?

An allele is a version of a gene that you inherit from one of your parents. Two alleles make a complete gene.1

Humans and other organisms that create offspring from two parents have genes that are made of two alleles.

One allele is inherited from each parent. For example, if your mother has brown eyes, you might inherit a brown eye allele. If your father has eyes of a different color, you might get a different allele.

How Do Alleles Differ from Genes?

Alleles are just versions of a gene. Both terms technically refer to the same series of proteins, but their usage in biology differs.1

You would use the term “gene” to describe sections of DNA or a DNA sequence. If you must differentiate between the form of a gene inherited from each parent, you would use “allele” to talk about the allelic variation.


An allele is a specific version of a gene, so you will always have two alleles in a gene. These contribute to your traits.

The Role of Alleles in Determining Traits

The alleles you inherit from your parents determine many of your physical and personality traits. However, it’s more complex than inheriting alleles for simple things like hair color and even more complicated things like the propensity for bad teeth.

Understanding Genetic Mutation

Mutation” is often misunderstood by popular culture. The word brings to mind creatures rapidly transforming or having strange physical characteristics. In genetics, mutation simply means the slight changes in genes and alleles as they are passed down.

What's the Difference Between Genes and Alleles? 2

As cells divide, they also make copies of DNA. Over the course of millions of cell divisions, slight adjustments will likely occur. Think of it as copying a page of text a million times by hand—your handwriting will be slightly different sometimes.

These variations are already considered mutations. Eventually, changes that accumulate on a chain of copied genes create a distinct allele. Mutations also have a role in natural selection and increasing the survival rate of a species.


A genetic mutation isn’t necessarily a bad thing; it’s just a small adjustment in the gene as it gets passed down. The replication process doesn’t always copy the gene perfectly, so there will be some changes down the line.

How Do Alleles Determine Traits?

DNA is the complete set of instructions for a creature’s cells. Because your alleles carry these DNA sequences, they don’t just tell cells how to divide or how much of each type of cell to make. They also contain instructions for how you will look and even behave.

These instructions determine your traits, like your physical characteristics and personality. Physical traits include height, skin color, hormone levels, and propensity toward certain diseases.

Personality traits are a little more complex, as your personality is often determined by a complex interplay of several genes and even your environment. However, there are some personality or behavioral traits that you can inherit, such as:

  • Neuroticism
  • Vulnerability to mental health disorders
  • Ability to focus, which is often linked to serotonin production

The differences between physical traits are dependent on what mutant alleles you have. Having alleles that tell your cells to grow black hair causes you to have black hair, and so on.1

What are Dominant and Recessive Alleles?

Alleles are also classified as either dominant or recessive. For each allele pair you inherit from your parents, whether these alleles are dominant or recessive determines what trait you inherit from each parent.1

Dominant alleles ensure that the trait they are related to is expressed. The brown eye allele is dominant, so if you have it, you will likely have brown eyes.

Recessive alleles express their trait only when there is no dominant allele present. Blue eye alleles are recessive, so if you have both the brown and blue eye alleles, you will still have brown eyes.

Some examples of dominant alleles are:

  • Freckles are a dominant allele and will be expressed even if only one copy of the genetic variant is inherited
  • Tongue rolling is dominant and those who have inherited it will be able to fold their tongues into a U-shape
  • Curly hair is a dominant trait and will be expressed over straight hair

Some examples of recessive alleles are:

  • Albinism is a lack of pigment in the skin, caused by two copies of the mutated allele
  • Attached earlobes are when the lobes of the ear do not dangle and are instead attached to the skin, you need two copies of this allele to express it
  • Sickle cell anemia is a recessive disorder that needs two mutations to develop
What's the Difference Between Genes and Alleles? 3


A dominant allele is an allele that will be expressed even if there’s only one copy of it. A recessive allele is an allele that will only be expressed in the absence of a dominant allele—essentially if there are two recessive copies.

What are Inheritance Patterns?

An inheritance pattern determines whether a trait is passed down or not. It’s how you determine whether a genetic condition will be passed from one generation to the next.

There are three types:

  • An autosomal dominant inheritance pattern means that a trait or disease is linked to the dominant variant of a gene. The same trait can usually be seen in every generation. It is also considered a dominant phenotype.
  • An autosomal recessive inheritance pattern means that the trait is linked to a recessive gene. A person must inherit a recessive allele from each parent for this trait to be expressed. This also means that the recessive allele can exist in a parent’s DNA even when they don’t show the trait.
  • An X-linked inheritance pattern means the trait is linked to an allele on the X chromosome. In other words, this is a sex-linked characteristic.


An inheritance pattern is what dictates whether or not a trait will be expressed in your offspring. There are three types:

  • Autosomal dominant – This trait is seen in every generation, as it only needs one copy to be expressed
  • Autosomal recessive – This kind of trait is rare or even “skips” generations because it’s only observable when there is no dominant allele
  • X-linked – These types of traits are only connected to the X chromosome

What is a Gene Locus and How Does it Relate to Alleles?

Gene locus refers to a specific location along a gene or DNA sequence.2 When studying a particular gene, noting the gene locus helps scientists track specific alleles. It’s like saying “the hundredth line of code” or “page 176 of the book.”

When scientists examine chromosomes under a microscope, genes look like actual elongated shapes.

These shapes come in pairs—one from the biological mother and the other from the biological father. With a gene’s given genomic location, it is easier for scientists to visually examine alleles.


A gene locus is a specific section of a gene you’re looking at. It’s like dictating directions or specific areas to refer to.

What is the Human Genome Project?

The Human Genome Project was an international research project that mapped out all of the genes in human DNA. This essentially means creating a complete list of all the gene locuses in human DNA. The project was started in 1990 and completed in 2003.3

This means that we now know the complete code for human DNA. This does not, however, mean that we can account for all different versions or variant forms of genes yet. It also does not mean that scientists have the ability to predict every trait an individual inherits.

Ongoing genetic research around diseases and biological function revolves around now finding connections between genes and their effects on the body.


The Human Genome Project is a project that hopes to map out all the genes in human DNA to better understand it. Research continues today to fill gaps in genealogical and medical research.

What Are Phenotypes and Genotypes?

Genotype refers to what versions of genes you have. Phenotypes refer to the physical characteristics an organism’s genotype produces.

How Do Alleles Influence Phenotypes and Genotypes?

The variant forms of your alleles make up your complete genotype. It is usually not the case that any single gene actually informs your eventual physical attributes. Instead, your whole genotype comes into play in a complicated manner.

For example, it is not a specific gene that controls skin pigmentation. Different alleles affect different things in your body that produce your skin color.

These could be alleles that determine how much melanin your body makes, over 150 of them, to be exact. These could be alleles that even affect your ability to metabolize sugar.

An organism’s phenotype is any of such affected physical characteristics. You have a phenotype for your height, hair color, eye color, blood type, and more.

What's the Difference Between Genes and Alleles? 5


A genotype is all the genetic material in an organism and which versions of genes you have in your genetic makeup. A phenotype is the physical characteristics that are expressed based on your genotype.

Your alleles make up your genotype, and your phenotype is determined by which allele is expressed.

The Role of Alleles in Medical Genetics

Multiple alleles interact to affect such things as your propensity for disease. Everything from your hormone production to your metabolism is affected by multiple alleles.

Genetic variations in your alleles can be so drastic that they can cause genetic diseases. These genetic mutations are called “pathogenic,” meaning they are harmful instructions for your body.4

In some cases, a person may even have a missing or extra chromosome in their DNA which can severely affect their physical traits.4

What are the Types of Genetic Disorders?

There are three categories of genetic disorders:

  • Chromosomal genetic disorders – Caused by a missing or extra chromosome. Some examples are Down syndrome, Klinefelter syndrome, and more. 
  • Complex genetic disorders – Caused by multiple pathogenic mutations. These can even be caused by a pregnant mother’s exposure to substances like tobacco or alcohol, as well as mutations passed down the family tree. Diseases such as arthritis, Alzheimer’s disease, cancer, diabetes, and autism are highly correlated with genetics.
  • Single-gene disorders – Caused by a single mutant allele. Sickle cell disease, cystic fibrosis, and congenital deafness are some examples.


The interplay of several genes or alleles is what determines your propensity for any disorders, how you digest, and even your likelihood of addiction. It’s a complex interplay, but genetics is a big contributing factor.

Genetic disorders are illnesses you may inherit and develop. There are three types:

  • Chromosomal – This is due to missing or an extra copy of a chromosome
  • Complex – This requires several mutations to be inherited and expressed
  • Single-gene – Just one copy of a mutant allele is required for these to be expressed

How Do Alleles Play a Role in Sex-Linked Traits?

Humans have 22 numbered gene pairs and one pair known as the sex-linked chromosomes. These are labeled the X chromosome and Y chromosome, and they contain the alleles that affect sexual characteristics.5

Biological males in humans have an X and a Y chromosome. Biological females have two X chromosomes instead. This also means that the offspring of a male and female parent will always inherit one X chromosome from their mother and either an X or Y chromosome from their father.5

Despite having two X chromosomes, biological females are less susceptible to having diseases with an X-linked inheritance pattern. This is because the second X chromosome can act as a backup set of instructions that make up for the deviation of the affected chromosome.5

However, because those born male only have one X chromosome, they are more likely to be affected by any X-linked genetic disorder.

What's the Difference Between Genes and Alleles? 6

Some X-linked traits and disorders are:

  • Duchenne Muscular Dystrophy
  • Fragile X Syndrome
  • Hemophilia A and B
  • Red-Green Color Blindness
  • Klinefelter Syndrome
  • Triple X Syndrome

Some Y-linked traits and disorders are:

  • Excessive hair growth in the ears
  • Webbed toes
  • Likelihood of tumor growth
  • Artery health

Take note that Y-linked traits and disorders are only passed down to males in a lineage, as only biological men can pass down and inherit a Y chromosome.


Sex-linked traits are traits tied to the X and Y chromosomes, or simply the sex chromosomes. X-linked traits and disorders are passed down to all children, while Y-linked traits and disorders can only be passed down and inherited by biological males, as only they have Y chromosomes.

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Updated on March 18, 2024
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5 sources cited
Updated on March 18, 2024
  1. Alleles” National Human Genome Research Institute (NIH).
  2. Locus” National Human Genome Research Institute (NIH).
  3. The Human Genome Project” The Human Genome Project.
  4. Genetic Disorders” Cleveland Clinic.
  5. Sex Linked” National Human Genome Research Institute (NIH).
Will Hunter
Will Hunter
Content Contributor
Will is a content writer for KnowYourDNA. He received his B.A. in Psychology from the University of California, Los Angeles. Will has 7 years of experience writing health-related content, with an emphasis on nutrition, alternative medicine, and longevity.