Hearing loss can be caused by environmental or genetic factors. In around 60% of children with isolated (non-syndromic) hearing loss, a genetic cause can be identified by genomic testing.
This webpage is a guide for paediatricians and otolaryngologists who want to learn more about ordering genomic testing for children with non-syndromic hearing loss. Bookmark it to keep it handy.
In this document, we refer to individuals as ‘deaf or hard of hearing’ and use the term ‘hearing loss’ as a noun to describe the condition affecting individuals who are deaf or hard of hearing. This resource has been reviewed by the Australian Childhood Deafness Community Advisory Group.
Please note: This information is not intended to replace personalised patient advice from a genetics expert.
This page is specific to genomics for hearing loss. If you are after general information, please refer to our genomics explainers.
- How is genomics used in the care of children with hearing loss?
- When should I consider genomic testing for a deaf or hard of hearing child?
- Is genomic testing right for this family at this time?
- What genetic and genomic tests are available for childhood hearing loss?
- What is the Medicare eligibility criteria?
- How do I order a genomic test?
- What do I need to know about informed consent?
- How do I interpret and disclose genomic test results?
- How much will it cost for the child and family?
- What does genomic testing mean for family members?
- Resources to use in clinic
How is genomics used in the care of children with hearing loss?
Genomic testing is used to identify genetic causes for hearing loss. Genetic causes for hearing loss can be inherited from the child’s biological parents or may have developed in the child for the first time.
Genomic testing can:
- Identify the underlying genetic cause of a child’s hearing loss
- Provide additional information regarding the hearing loss diagnosis and prognosis, for example, whether the hearing loss is expected to be stable or progress over time
- Confirm whether the hearing loss is non-syndromic or syndromic (i.e. whether there are other expected medical or health needs)
- Enable access to tailored medical management
- Give family members the opportunity to access genomic testing in the context of their child’s hearing loss
- Inform recurrence risk for future pregnancies and allow families to access prenatal genetic counselling
- Enable possible access to gene therapies where available or appropriate (an emerging treatment)
When should I consider genomic testing for a deaf or hard of hearing child?
When a child is diagnosed with hearing loss, you may consider offering genomic testing. Talking to the family can help you gauge what they understand about genetics, whether they are interested in the test, and how useful they think genomic testing may be.
Some families may not want to receive the information a genomic test provides. They may prefer to wait until their child is an adult before making decisions about genomic testing. Other families may think genomic testing is helpful in caring for their child and provides them with detailed information or helps them prepare for the future.
Is genomic testing right for this family at this time?
Communication with the family is the most important tool for gauging whether genomic testing is right for them. This may involve direct questions about the family’s preferences as well as non-verbal cues such as body language or emotional responses.
Ask yourself the following when considering genomic testing:
Medical utility for the child
- Could genomic testing identify an undiagnosed medical condition that explains the child’s hearing loss?
- Could genomic testing provide prognostic information about the child’s hearing loss?
- If the child already has medical and social supports in place, what will a genomic result add?
Reproductive planning
- Is this family planning on having more children?
- How does the family feel about the potential of having another child with hearing loss?
- How do the family’s values influence their reproductive preferences?
- Is this family seeking genetic information for the purpose of IVF and pre-implantation genetic testing/diagnosis or prenatal testing?
- Does this family have relatives who would benefit from genetic information?
Psychosocial impact
- How is the family coping with the knowledge that their child has hearing loss?
- Does the family need more time to process information before genomic testing occurs?
- Would genomic testing exacerbate feelings of guilt/anxiety, or could it contribute to closure/empowerment?
Values and culture
- Are there multiple decision makers in this family who should be involved in the decision? If so, should the decision be postponed or additional appointments made?
- What community supports does this family have? What communities or peer support networks are the family part of, and what could this indicate about their values or views on genomic testing for hearing loss?
- Does this family use Auslan or other languages? Would they benefit from an interpreter to ensure they fully understand the implications of genomic testing?
What genetic and genomic tests are available for childhood hearing loss?
Connexin testing
The two genes most commonly associated with non-syndromic hearing loss are GJB2 and GJB6. These genes encode connexins, which are proteins involved in the formation of gap junctions within the inner ear. Changes – also known as variants – in these two genes can disrupt the conversion of external sound waves into electrical impulses that are projected to the brain, causing sensorineural hearing loss.
This test checks for variants in the two genes. Changes in the connexin genes can cause any degree of sensorineural hearing loss ranging from mild to profound. Hearing loss of this kind is usually non-progressive and without any associated medical comorbidities. However, depending on the variant, hearing loss can worsen over time.
This article in GeneReviews explains GJB2-related autosomal recessive non-syndromic hearing loss in further detail.
Whole exome sequencing
Medicare now funds genomic testing for children with non-syndromic hearing loss. Genomic testing can be ordered by paediatricians, ENT specialists, geneticists and any medical specialists with expertise in managing childhood hearing loss.
Two kinds of tests are funded:
- Singleton testing, where only the child is tested (MBS item 73440)
- Trio testing, where the child and their biological parents are tested (MBS item 73441)
These tests are comprehensive and reduce the number of tests a child has to undergo. They include copy number variant analysis, which looks for deletions or duplications, and sequencing of the genes associated with non-syndromic hearing loss, including connexins. A patient does not need a negative connexins result to be eligible for these tests. Read below for more information on eligibility.
Genomic testing for childhood syndromes
If a child has syndromic features in addition to their hearing loss such as dysmorphic facial features, congenital anomalies, intellectual disability or global developmental delay, then they may be eligible for Medicare-funded genomic testing for childhood syndromes.
What is the Medicare eligibility criteria?
Medicare funds genomic testing for hearing loss if the patient meets the following criteria:
- The individual has congenital or childhood-onset hearing loss that presented before 18 years of age
- Hearing loss is permanent (bilateral or unilateral) and is moderate, severe or profound (>40dB in the worst ear over 3 frequencies)
- Hearing loss is classified as sensorineural, auditory neuropathy or mixed
View the eligibility criteria in full:
- Singleton testing, where only the child is tested (MBS item 73440)
- Trio testing, where the child and their biological parents are tested (MBS item 73441)
How do I order a genomic test?
Different laboratories will have different test ordering procedures. Check your laboratory’s website or reach for more information on the test you would like to order, and the specimen required.
Medicare-funded genomic testing may only be available in selected laboratories. Contact your local laboratory if you are unsure. This short guide for paediatricians and ENTs can help you understand how to order this test.
The Victorian Clinical Genetics Services is the main laboratory that offers connexin testing and whole exome testing for hearing loss in Victoria.
What do I need to know about informed consent?
Informed consent
Consent for genetic and genomic testing follows the same principles of consent for all clinical practice in Australia. Australian Genomics has a range of consent form resources on their website to support an informed consent discussion, including the following:
- Consent form for clinical genomic testing (parent/guardian)
- Patient fact sheet on genetic and genomic testing
- Health professionals guide for obtaining consent
Obtaining informed consent from a family is important when ordering any genetic test. Clinicians should tailor these conversations depending on the type of test they are ordering, the potential outcomes of the test and the potential implications for family members. Families can choose whether they are willing to be contacted about research in the future.
Children require a guardian to consent on their behalf, but the extent to which you involve a child depends on their age and decision-making capacity. This is up to the discretion of the clinician. Clinicians should involve and engage young children and teenagers to help them understand what genomic testing is in an age-appropriate manner.
Insurance
Genomic testing and life insurance is a component of consent which can be tricky for clinicians to navigate. Insurance issues do not impact the majority of people considering genomic testing. This fact sheet explains how genetic and genomic testing may impact an individual's insurance policies.
Many life insurance companies have agreed to a moratorium that limits the use of genetic test results when assessing life insurance applications. Here are the key facts.
How do I interpret and disclose genomic test results?
Laboratories will provide reports explaining the results of the genomic test ordered. There are four possible outcomes of a genomic test:
- Positive: a variant is found that explains the condition
- Uncertain: a variant is found but it is not clear whether it explains the condition
- Negative/uninformative: No variant is found to explain the condition
- Incidental finding: A disease-causing variant is found in a gene not related to the condition
The laboratory report will include details about the patient’s genetic variant(s), the type of variant(s) and the evidence available regarding classification of the variant(s).
Laboratories follow the American College of Medical Genetics criteria for classifying variants on a scale of benign to pathogenic (disease-causing), as seen below.
| Classification | Class | Probability that the variant causes the condition |
|---|---|---|
| Pathogenic | Class 5 | >99% |
| Likely pathogenic | Class 4 | 90-99% |
| Uncertain significance (VUS) | Class 3 | 10-90% |
| Likely benign | Class 2 | 0.1-10% |
| Benign | Class 1 | <0.1% |
Reports may also include information about recommended next steps, such as testing additional family members or providing genetic counselling to the family. The ACMG also has guidelines on clinical actions for a given variant classification, as summarised in the table below.
| Classification | Clinical actions | |
|---|---|---|
| Pathogenic | Class 5 | Cause for condition identified Can be used to direct management Can be used for family planning Can be used for predictive testing |
| Likely pathogenic | Class 4 | Cause for condition likely been identified May be used to direct management May be used for family planning May be used for predictive testing in other family members |
| Uncertain significance | Class 3 | Cause for condition still unclear Cannot be used to direct management Cannot be used for family planning Cannot be used for predictive testing in other family members If there is potential clinical significance, perform segregation and functional studies |
How much will it cost for the child and family?
The cost of genomic testing for hearing loss will depend on the laboratory providing the test and whether the child is eligible for the Medicare item number. Contact your local laboratory for more information.
What does genomic testing mean for family members?
Because biological family members share DNA, a genomic test result may have implications for other family members. If a genetic cause for hearing loss is found, the implications for family members depends on the specific diagnosis and its inheritance pattern. Non-syndromic hearing loss is usually inherited in an autosomal recessive pattern. This means there is a genetic change in both copies of the gene which is associated with hearing loss.
Parents of someone with a recessive condition are usually both unaffected carriers of the specific gene change. For example, if a child is diagnosed with an autosomal recessive genetic condition such as GJB2-hearing loss, it is likely that both parents are unaffected carriers for the same condition. You can confirm this by arranging parental testing, which will also confirm whether the child’s variants are in trans, meaning that the genetic changes exist on separate copies of the gene involved.
If carrier parents conceive naturally, each pregnancy has a one in four chance of inheriting genetic changes on both copies of the gene (causing hearing loss), a one in two chance of inheriting a change on one copy (carrier status) and a one in four chance of having two normal copies of the gene. This may be important when the couple's children are planning their own families. Once a genetic variant has been found in a family, cascade testing and genetic counselling may be available for extended relatives.
Resources to use in clinic
Aussie Deaf Kids has a number of resources to support families and build their knowledge, including an explainer on genetic inheritance.
The Centre for Disease Control has parent guides to hearing loss.
This Centre for Genetics Education resource explains autosomal recessive inheritance.
Deaf Children Australia has a range of programs and resources available.
Harvard Medical School has a guide to understanding the genetics of deafness for patients and families.
The National Deaf Children’s Society in the UK offers information and support.
NSW Health has a fact sheet on the inheritance of hearing loss and deafness.
The Victorian Clinical Genetics Services has a fact sheet on genomic testing for patients.