Copy Number Variants – Benign or Pathogenic – a complex issue


Molecular cytogenetics offers the opportunity to recognize the smallest changes in the human karyotype. These methods show that the karyotype is not as stable as previously thought. Almost every person has small deletions or duplications, involving different areas of the genome. These small anomalies collectively are called copy number variants (CNV). These CNVs may involve one or several genes or may contain only gene-free areas of DNA. CNV may be sporadic or may be inherited. Currently all CNVs are divided into 3 groups:

  1. Benign CNV;
  2. CNVs of unknown (or uncertain) significance (VOUS);
  3. Pathogenic CNV.

Benign CNVs are mostly small (less than 0.2 Mb) deletions or small (less than 0.5 Mb) duplications, which do not include any genes or include genes, which do not cause any disorders. Most pathogenic CNVs are relatively large (more than 1 Mb) and include several genes. If any CNV is repeatedly found in association with a certain phenotype (for example, seizures or autism) such a CNV is considered as pathogenic. Deletions and duplications of chromosomes 15q13.3, 16p11.2, and 16p13.11 are examples of pathogenic CNV. VOUS are CNV, when it is not yet clear whether these variants are benign or may cause pathologic conditions. Further studies are necessary to reassign these CNV into “pathogenic” or “benign” classes.

In some families the same CNV which was found in a child with a clinical abnormality (for example, a heart defect or developmental delay) is found in one of his/her parents. Sometimes this parent is also affected (usually with milder clinical manifestations), but in most cases the carrier parent is absolutely healthy. It raises a question: how to explain that a child with a given CNV has some pathology, but his/her parent with the same CNV does not.

This explanation will be different for “benign” CNV and “pathogenic” CNVs. Benign CNVs are not related to any disorders. However, some authors just report all CNVs found in the specific group of patients (for example, patients with tetralogy of Fallot or cleft palate) but do not classify these CNVs into the sub-groups. The same situation may occur when a family considers a CNV found in a child as a cause of his/her disorder. Actually, however, if this CNV is benign it has no connection with child’s abnormality. It is evident that the same CNV may be found in a healthy parent. When a CNV is found in the examined child, all families have to ask whether this CNV is benign or pathogenic. If a CNV is benign we have to look for other explanations of the child’s disorder.

Explanations of the occurrence of a pathogenic CNV in a healthy parent are not so easy. To be honest, the nature of this phenomenon is not always clear. In most families, however, it is caused by participation of other genetic factors. The easiest example: assume that a healthy mother has a microdeletion of chromosome 16p13.11 involving the NDE1 gene, known to cause a severe autosomal-recessively inherited brain disorder. The non-deleted copy of this gene in this woman is normal. She transmits this deletion to her son. But if the healthy father of this child has a mutation in the same gene he can transmit the mutated copy to his son. In this case the child having a maternal CNV and a paternal mutated gene will develop an autosomal-recessive brain disorder. Several dozens of similar situations have been reported so far in the literature. But this explanation covers only a small fraction of cases where a healthy parent has the same CNV as his/her affected child. Another explanation presumes the influence of other genetic factors somehow controlling the expression of the pathogenic CNV. For example, small deletions 1q21.1 may produce a very serious condition – TAR syndrome (thrombocytopenia – absent radius) if the patient also inherits a small specific non-coding area of DNA. Sometimes regulatory genes may directly affect expression of the “critical” genes. And we cannot exclude the phenomenon of incomplete penetrance known in numerous dominant disorders, when a person having a mutant gene has no clinical manifestations. It is not clear yet whether some environmental factors may affect expression of CNVs.

CNV is a relatively new topic in human cytogenetics, and there are many white spots regarding the role of these microdeletions and microduplications in humans.

Is it reasonable to test small brothers and sisters of the child with pathogenic CNV if this CNV is inherited from the healthy parent? The results of the test will not change health of the child but (if the test is positive) may add a psychological burden. When the child reaches child-bearing age this testing may become more reasonable, especially if we know not only the possible clinical consequences of the given CNV, but also know the proportion of the affected persons among all carriers of the given CNV.

Dr. Iosif Lurie, Medical Geneticist, CDO Medical Consultant

10 Ways to Celebrate Rare Chromosome Disorder Awareness Week


PURCHASE and wear with pride your new RCDAW t-shirt.

ORGANIZE a RCDAW event. The event organizer and their child receive free t-shirts. The event could be a “dress down for a dollar” day, bake sale, dine-around at a local restaurant (portion of proceeds to CDO), or something else.

PARTICIPATE in CDO’s sibling poetry contest. Send poems (with first name and age of author) to or post on our Facebook page. Winner receives a RCDAW t-shirt.

CUSTOMIZE the new RCDAW logo to include your child’s picture.

VISIT the CDO website for all the latest information and news…

SHARE the CDO link with Facebook friends and Twitter followers.

READ a book to your child that celebrates everyone… for example, Special People Special Ways by Arlene Maguire.

WRITE a letter to your congressperson expressing your support for the 21st Century Cures Act.

POST on Facebook or send a Tweet every day for the week describing how your child with a chromosome disorder is courageous, determined, optimistic, and more.

EMAIL information and a photo of your child to CDO at (diagnosis, likes, daily accomplishments, etc.). We will feature several children each day on Facebook, Instagram and Twitter during the week of June 7-13.

Chromosome Disorder Outreach Inc. is a non-profit organization providing information and support to all those coping with a rare chromosome disorder diagnosis.  Whether this diagnosis is received prenatally or as an adult, CDO will always be there to help.