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”.
Second Tokyo Clinical Laboratory’s next-generation sequencers report test results when there are deletions or duplications of 7 million bases (7 Mb)
or more.

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.

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

ChromosomeDeleted PortionSyndromeRemarks
11p12Alagille syndrome 
11q21.11q21.1 microdeletion syndrome 
11p361p36 deletion syndromeFrequency of occurrence (at birth) 1 out of 4,000 to 10,000 cases.
Growth difficulties, severe mental retardation, intractable epilepsy, and other conditions.
22q13Nephronophthisis Type 1 
22p21Total anterior encephalocele 
22q37.3Albright’s syndrome-like metacarpal and metatarsal shortening 
33q293q29 microdeletion syndrome 
44p16.3Wolf-Hirschhorn syndromeFrequency of occurrence (at birth) 1 out of 50,000 cases.
Severe mental developmental delay, growth problems, intractable epilepsy, multiple morphological abnormalities.
55p13.2Cornelia de Lange syndrome 
55p15.2Cri-du-chat SyndromeFrequency 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
55q35.3Sotos syndromeSome differences in symptoms between the deletion and duplication types have been reported.
Frequency of occurrence (at birth) 1 of 14,000 cases.
77q11.23Williams syndrome 
77p13Pallister-Hall syndrome 
77p14.1Greig Cephalopolysyndactyly Syndrome 
77p21.1Saethre-Chotzen syndrome 
77q36.3Total Anterior Encephalocele Type 3 
88q12.2CHARGE syndrome 
88p23.18p23.1 microdeletion syndrome 
88q23.3Trichorhinophalangeal Syndrome Type 1 
8番8q24.11Langer-Giedion syndrome 
1111p11.2Potocki-Shaffer syndrome 
11番11p13WAGR syndrome 
1212q24.13Noonan syndrome1 case of duplication and 1 case of deletion reported in RAF1
1313q14.2Retinoblastoma, developmental delay 
1313q32.3Total anterior encephalocele type 5 
1515q11.2〜q13Prader-Willi syndromeDeletion 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
1515q11.2〜q13Angelman syndromeOccurs 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.
1616p11.216p11.2 microdeletion 
1616p13.1116p13.1 microdeletion 
1616p13.3Rubinstein-Taybi syndromeFrequency of occurrence (at birth) 1 out of 125,000
1717p13.3Miller-Dieker syndrome 
1717p11.2Smith-Magenis syndromeFrequency of birth (at birth) 1 out of 15,000~25,000 cases
1717q11.2Neuroblastoma Type 1 
2020p12.23Alagille syndrome 
2222q11.2DiGeorge 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.
2222q13.33Phelan-McDermid syndrome 

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Chromosome Duplication

ChromosomeDuplicated PortionSyndromeRemarks
11q21.11q21.1 microduplication syndrome 1q21.1 Partial duplication(Back translation)
22p21Total anterior encephalocele 
33q293q29 microduplication syndrome 
55p13.2Cornelia de Lange syndrome  
55q35.3Sotos syndromeSome differences in symptoms between the deletion and duplication types have been observed.
88p23.18p23.1 microduplication syndrome 
99q34.13Tuberous sclerosis type 1Caused by the TSC1 gene.
1 out of 5,800 cases.
1010q24.310q24 duplication syndrome 
1111p11.2Potocki-Shaffer syndrome 
1111p13WAGR syndrome 
1212q24.1Noonan syndrome1 case of duplication and 1 case of deletion reported in RAF1
1313q32.3Total anterior encephalocele type 5 
1515q11.2〜q13Prader-Willi syndromeDeletion 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.
1515q11.2〜q13Angelman syndromeOccurs 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.
1515q26qterOvergrowth and intellectual disability 
1616p11.216p11.2 microduplication 
1616p13.3Tuberous sclerosis type 2Caused by the TSC2 gene.
1 out of 5,800 cases.
1616p13.3Rubinstein-Taybi syndromeCaused by the CREBBP gene.
Frequency of occurrence (at birth) 1 out of 125,000 cases
1616p13.1116p13.1 microduplication 
1717p11.2Potocki-Lupski syndrome Chromosome 17 (17p11.2) partial duplication: Duplication in children with developmental delay
1717p12Charcot-Marie-Tooth disease, type 1A 
1717q21.31b17q21.31 microduplication syndrome 
2222q11.1Cat’s eye syndrome 
2222q11.222q11.2 Duplication syndromeCongenital 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 Second Tokyo Clinical Laboratory cannot detect deletions or duplications of 7 million bases or less.
Not all cases of the syndrome can be detected.

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