Variant profiling in practice

PALB2 variant profilingIn my last blog I introduced the concept of variant profiling. This is a way to navigate through the sea of genetic test data to find genetic variants with health impacts.

Variant profiling involves defining the type of variant that can cause a disease taking into account the characteristics of the gene, the disease and how variants in the gene can cause the disease.

When a genetic test is performed, variants that match the pathogenic variant profile are prioritised for evaluation, starting with variants that have the closest match.

I wanted to give you an example of variant profiling in practice.



PALB2 is a cancer predisposition gene. We each have two copies of the PALB2 gene. People born with one PALB2 gene not working have an increased risk of breast cancer as adults. People born with both PALB2 genes not working have a severe childhood condition called Fanconi Anemia (type N).

PALB2 genetic testing is now regularly performed in individuals with breast cancer, or at risk of breast cancer. PALB2 variants are often found in these tests and have to be evaluated. This can be very time-consuming, particularly for the variants that switch one amino acid for another (known as nonsynonymous or missense variants). Unfortunately, even after detailed review, PALB2 nonsynonymous variants that are absent or rare in databases are typically classified as ‘variants of uncertain significance’, or VUS for short. This means the laboratory interpreting the test believes there is insufficient information to make any judgement about whether the variant is pathogenic or benign.


Variants of uncertain significance are often mismanaged

Today, there are more than 600 PALB2 variants in the ClinVar database that have been reported as a ‘variant of uncertain significance’.

Given the potential negative consequences of saying a variant is ‘of uncertain significance’, it is vitally important the term is used sparingly.

Cancer geneticists recommend that individuals with a VUS should be managed in the clinic in the same way as individuals without a pathogenic variant. However, it is well recognised that often the reverse happens. People with a VUS are, not infrequently, managed in the same way as people with a pathogenic variant. Why this occurs is complex and I will discuss it in another blog. But it can have very serious consequences, including entirely healthy women having their entirely healthy breasts removed. Or couples being incorrectly advised about their risk of having a child with a serious genetic disease.

Given the potential negative consequences of saying a variant is ‘of uncertain significance’, it is vitally important the term is used as sparingly as possible. And we need to be particularly careful to ensure that likely benign variants are not called ‘variants of uncertain significance’.

The VUS rate for PALB2 for most labs is ~20%.

The VUS rate for PALB2 in our lab is 0%.

Variant profiling has made our PALB2 variant interpretation better, faster, more automated and more useful to patients and doctors.


Truncating PALB2 variants are pathogenic

The first step in the variant profiling is to consider the types of variants that cause disease. If you are unfamiliar with the different types of gene variants please read our blog about it. For PALB2, studies have consistently shown that loss-of-function truncating PALB2 variants are pathogenic. This includes truncating variants right at the end of the gene. We recently reviewed this in our lab, testing PALB2 in 3906 women with breast cancer and 2096 population controls. We found truncating PALB2 variants in 58 women with breast cancer and in 1 control (P=4×10-10). There were many different truncating variants, and many were only present in one person. It is only through the mechanistic understanding that loss-of-function PALB2 variants cause disease that we can classify any loss-of-function PALB2 variant as pathogenic, even if it has never been seen before.


Non-truncating PALB2 variants are likely benign

So we have established that all PALB2 truncating variants are pathogenic. What about the non-truncating variants. In particular the nonsynonymous (missense) variants that switch one amino acid for another.

To date, after 10 years of testing and research, no non-truncating PALB2 variant has been shown to be pathogenic. In our recent analysis the frequency of nonsynonymous PALB2 variants in the breast cancer cases was no different from the controls, as shown in the image accompanying this blog. The actual variants were not the same, because individual variants are very rare. But considering the variants collectively, based on their impact, allows us to assign non-synonymous variants to the ‘likely benign’ category rather than calling them ‘variants of uncertain significance’.

Calling a variant ‘likely benign’ rather than ‘variant of uncertain significance’ greatly reduces the chance of mismanagement. And the chance that women will have inappropriate surgery or inappropriate terminations.


Variant profiling principles can be applied to any gene

I chose PALB2 as an example because it is the simplest gene to profile that we test. For PALB2 there is one profile characteristic – does the variant cause truncation – that can be used to categorise all variants. For almost all PALB2 variants this can be done computationally and automatically. Most disease genes are not so straight-forward. But the underlying principles of variant profiling are applicable to any gene and will likely be useful for any gene.

Leave a Comment

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.