What is all autosomal whole region partial deletion/duplication syndrome?

A chromosome that is missing a part is called a “deletion” and a chromosome that is partially increased is called a “duplication”. Tokyo Clinical Laboratory’s next-generation sequencers report test results when there are deletions or duplications of 7 million bases (7 Mb) or more.

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Microdeletion diseases can be manifested by deletions of as little as 1 to 3 million nucleotides, but some cases can involve more than 7 million nucleotides, including the gene in question. Large deletions beyond the disease-specific gene deletion may be associated with similar symptoms or more severe disease because the gene is defective. Therefore, we believe it is appropriate to give the same diagnostic name to a disease-specific deletion, even if it is large in extent, if it is included in the disease-specific region. Because the term “microdeletion” is misleading, we refer to it as “partial deletion disease” on this site.

  • 全常染色体全領域部分欠失疾患

    All autosomal regions

    Partial Deletion syndrome

  • 通常の染色体

    Normal

  • 全常染色体全領域部分重複疾患

    All autosomal regions

    Partial Duplication syndrome

Deletions and duplications can have a variety of symptoms depending on the function of the gene present in the area. For example, if a chromosome containing a gene that produces a certain type of enzyme is deleted, an enzyme deficiency is seen; if a chromosome containing a gene responsible for bone formation is duplicated, an abnormality of bone formation is seen.

Chromosome deletions and duplications were conventionally detected under a microscope by staining chromosomes with horizontal stripes, but this method could only detect deletions and duplications of approximately 10 million bases (10 Mb) or more. In recent years, more accurate testing has become possible with the use of next-generation sequencers and microarray chromosome testing. As a result, deletions and duplications do not occur only in specific chromosomes, but are found throughout the entire chromosome, and the symptoms of each site of abnormality are now known. The association between deletions and duplications and the accompanying clinical findings has been reported, and a database of genetic information on the abnormalities has been compiled. Some of these cases have been reported based on common abnormal regions and characteristic findings, and some have been placed as independent diseases, while others are rare or have never been reported before. Therefore, when a deletion or duplication is found that has not been reported to be associated with an independent disease, it is necessary to search case reports and genome databases for the individual symptoms that appear.

Cases with a 14.4 million base duplication of chromosome 7 have been reported to show abnormalities in the skeletal system, especially the spine and sacral tailbone, which are related to HLXB9, a homeobox gene involved in body formation. However, not all genes in the duplicated regions have been found to be associated with clinical findings. In some cases, deletions or duplications are found but do not cause any symptoms. This is the case when the deletion or duplication does not contain an important gene involved in vital functions or body formation, or when the gene is present but of a type that does not cause pathological findings. One such example is a duplication on the short arm of chromosome 8 (8p23.2) that spans 2.5 million bases (2.5 Mb) but is understood to be a normal mutation with no abnormal findings because only one tumor suppressor gene is located there. However, it is necessary to distinguish whether a deletion or a duplication is pathological or not, but it is impossible to make such a judgment if it has never been reported before. We hope you understand that we are unable to make such a diagnosis for those cases that have not been reported so far.

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Nameless Cases

These are examples of case reports of recently reported cases of all autosomal whole region part deletion and duplication diseases.

Reported Cases of Partial Deletion / Duplication
of all Autosomal Chromosomes

Chromosome Deletion

Chromosome Deleted Portion Syndrome Remarks
1 1p12 Alagille syndrome  
1 1q21.1 1q21.1 microdeletion syndrome  
1 1p36 1p36 deletion syndrome Frequency of occurrence (at birth) 1 out of 4,000 to 10,000 cases.
Growth difficulties, severe mental retardation, intractable epilepsy, and other conditions.
2 2q13 Nephronophthisis Type 1  
2 2p21 Total anterior encephalocele  
2 2q37.3 Albright’s syndrome-like metacarpal and metatarsal shortening  
3 3q29 3q29 microdeletion syndrome  
4 4p16.3 Wolf-Hirschhorn syndrome Frequency of occurrence (at birth) 1 out of 50,000 cases.
Severe mental developmental delay, growth problems, intractable epilepsy, multiple morphological abnormalities.
5 5p13.2 Cornelia de Lange syndrome  
5 5p15.2 Cri-du-chat Syndrome Frequency of occurrence (at birth) 1 out of 20,000-50,000 cases
Low birth weight, growth problems, high-pitched cat-like cries. Small head size, decreased muscle tone, and psychomotor development.
Chromosome 5 partial deletion: high-resolution mapping in cri-du-chat syndrome
5 5q35.3 Sotos syndrome Some differences in symptoms between the deletion and duplication types have been reported.
Frequency of occurrence (at birth) 1 of 14,000 cases.
7 7q11.23 Williams syndrome  
7 7p13 Pallister-Hall syndrome  
7 7p14.1 Greig Cephalopolysyndactyly Syndrome  
7 7p21.1 Saethre-Chotzen syndrome  
7 7q36.3 Total Anterior Encephalocele Type 3  
8 8q12.2 CHARGE syndrome  
8 8p23.1 8p23.1 microdeletion syndrome  
8 8q23.3 Trichorhinophalangeal Syndrome Type 1  
8番 8q24.11 Langer-Giedion syndrome  
11 11p11.2 Potocki-Shaffer syndrome  
11番 11p13 WAGR syndrome  
12 12q24.13 Noonan syndrome 1 case of duplication and 1 case of deletion reported in RAF1
13 13q14.2 Retinoblastoma, developmental delay  
13 13q32.3 Total anterior encephalocele type 5  
15 15q11.2〜q13 Prader-Willi syndrome Deletion of a gene of paternal origin, attributed to a gene of maternal origin
Frequency of occurrence (at birth) 1 out of 10,000-25,000 cases
Hypomuscularity, hypopigmentation, hypoplasia of external genitalia
15 15q11.2〜q13 Angelman syndrome Occurs due to loss of function of UBE3A
Frequency of occurrence (at birth) 1 out of 12,000 cases.
Severe mental developmental delay, epilepsy, ataxic movement disorder, behavioral abnormalities, sleep disturbances, hypochromia, and characteristic facial features.
16 16p11.2 16p11.2 microdeletion  
16 16p13.11 16p13.1 microdeletion  
16 16p13.3 Rubinstein-Taybi syndrome Frequency of occurrence (at birth) 1 out of 125,000
17 17p13.3 Miller-Dieker syndrome  
17 17p11.2 Smith-Magenis syndrome Frequency of birth (at birth) 1 out of 15,000~25,000 cases
17 17q11.2 Neuroblastoma Type 1  
20 20p12.23 Alagille syndrome  
22 22q11.2 DiGeorge syndrome Type 2
22q11.2 deletion syndrome
Frequency of occurrence (at birth) 1 out of 4,000 cases
Congenital heart disease, delayed mental development, distinctive facial features, immunocompromised, cleft palate/soft palate closure, nasal voice, hypocalcemia.
22 22q13.33 Phelan-McDermid syndrome  

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Chromosome Duplication

Chromosome Duplicated Portion Syndrome Remarks
1 1q21.1 1q21.1 microduplication syndrome 1q21.1 Partial duplication(Back translation)
2 2p21 Total anterior encephalocele  
3 3q29 3q29 microduplication syndrome  
5 5p13.2 Cornelia de Lange syndrome  
5 5q35.3 Sotos syndrome Some differences in symptoms between the deletion and duplication types have been observed.
8 8p23.1 8p23.1 microduplication syndrome  
9 9q34.13 Tuberous sclerosis type 1 Caused by the TSC1 gene.
1 out of 5,800 cases.
10 10q24.3 10q24 duplication syndrome  
11 11p11.2 Potocki-Shaffer syndrome  
11 11p13 WAGR syndrome  
12 12q24.1 Noonan syndrome 1 case of duplication and 1 case of deletion reported in RAF1
13 13q32.3 Total anterior encephalocele type 5  
15 15q11.2〜q13 Prader-Willi syndrome Deletion of a gene of paternal origin, attributed to a gene of maternal origin.
Incidence (at birth) 1 out of 10,000-25,000 cases.
Hypomuscularity, hypopigmentation, hypoplasia of external genitalia.
15 15q11.2〜q13 Angelman syndrome Occurs due to loss of function of UBE3A
Frequency of occurrence (at birth) 1 out of 12,000 cases.
Severe mental developmental delay, epilepsy, ataxic movement disorder, behavioral abnormalities, sleep disturbances, hypochromia, and distinctive facial features.
15 15q26qter Overgrowth and intellectual disability  
16 16p11.2 16p11.2 microduplication  
16 16p13.3 Tuberous sclerosis type 2 Caused by the TSC2 gene.
1 out of 5,800 cases.
16 16p13.3 Rubinstein-Taybi syndrome Caused by the CREBBP gene.
Frequency of occurrence (at birth) 1 out of 125,000 cases
16 16p13.11 16p13.1 microduplication  
17 17p11.2 Potocki-Lupski syndrome Chromosome 17 (17p11.2) partial duplication: Duplication in children with developmental delay
17 17p12 Charcot-Marie-Tooth disease, type 1A  
17 17q21.31b 17q21.31 microduplication syndrome  
22 22q11.1 Cat’s eye syndrome  
22 22q11.2 22q11.2 Duplication syndrome Congenital heart disease, delayed mental development, distinctive facial features, immunocompromised, cleft palate/soft palate closure, nasal voice, hypocalcemia.

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(Reported examples are part of partial deletion / duplication)
The next-generation sequencer used at the Tokyo Clinical Laboratory cannot detect deletions or duplications of 7 million bases or less.
Not all cases of the syndrome can be detected.