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3q29 Recurrent Deletion

Synonyms: 3q29 Deletion Syndrome, 3q29 Microdeletion Syndrome

, MHS, PhD, , MD, PhD, , MD, , PhD, and , MMSc.

Author Information

Initial Posting: .

Summary

Clinical characteristics.

3q29 recurrent deletion is characterized by global developmental delay and/or intellectual disability, and commonly, speech delay, and increased risk for neuropsychiatric disorders (including autism spectrum disorder, anxiety disorder, psychosis, and/or schizophrenia). Other common findings are failure to thrive and feeding problems in infancy that persist into childhood, heart defects (especially patent ductus arteriosus), gastrointestinal disorders (including gastroesophageal reflux disease), and dental abnormalities. To date findings in fewer than 50 affected individuals have been reported.

Diagnosis/testing.

The diagnosis of the 3q29 recurrent deletion is established by detection of the 1.6-Mb heterozygous deletion by chromosomal microarray at the approximate position of chr3:195998129-197623129 in the reference genome (NCBI Build 38).

Management.

Treatment of manifestations: Early speech and language therapy to address speech delays; physical therapy as needed to address fine and gross motor delays; individualized education program (IEP) for school-age children; care by a child psychiatrist/psychologist as needed for neuropsychiatric disorders; feeding therapy and consideration of gastrostomy tube as needed; routine management of dental caries, congenital heart defects, recurrent ear infections.

Surveillance: Continued assessment of feeding and nutrition, developmental milestones, cognitive development, and possible neuropsychiatric manifestations.

Evaluation of relatives at risk: Parents and older and younger sibs of a proband should be tested for the 3q29 recurrent deletion to encourage close assessment/monitoring of developmental milestones (in children) and monitoring for neuropsychiatric manifestations (in children and adults).

Genetic counseling.

The 3q29 recurrent deletion is inherited in an autosomal dominant manner. Although most deletions are de novo, inherited deletions have been reported. If the 3q29 recurrent deletion identified in the proband is not identified in one of the parents, the risk to sibs is low (<1%) but greater than that of the general population because of the possibility of parental germline mosaicism for the deletion. Once the 3q29 recurrent deletion has been identified in an affected family member, prenatal testing for a pregnancy at increased risk and preimplantation genetic diagnosis are possible options.

Diagnosis

3q29 recurrent deletion is characterized by the (almost universally present) clinical features of developmental delay and/or intellectual disability; however, no single clinical feature distinguishes this condition from other similar conditions.

Suggestive Findings

The 3q29 recurrent deletion should be considered in individuals with the following clinical findings [Glassford et al 2016]:

  • Global developmental delay or intellectual disability, including speech delay
  • Autism spectrum disorder (ASD)
  • Slight facial dysmorphology, including a long, narrow face; short philtrum; high nasal bridge; and large ears [Ballif et al 2008]
  • Failure to thrive, failure to gain weight, and/or feeding problems in infancy that persist into childhood
  • Heart defects, especially patent ductus arteriosus
  • Gastrointestinal disorders, including gastroesophageal reflux disease (GERD)
  • Dental abnormalities

Of note, most individuals with the 3q29 recurrent deletion are identified by chromosomal microarray (CMA) analysis performed in the context of evaluation for global developmental delay, intellectual disability, and/or ASD.

Establishing the Diagnosis

The diagnosis of the 3q29 recurrent deletion is established by detection of the 1.6-Mb heterozygous deletion at chromosome 3q29, typically by chromosomal microarray (CMA).

For this GeneReview, the 3q29 recurrent deletion is defined as the presence of a recurrent 1.6-Mb deletion at the approximate position of chr3:195998129-197623129 in the reference genome (NCBI Build 38).

This is a recurrent deletion, mediated by non-allelic homologous recombination (NAHR) between segmental duplications (or low-copy repeats) flanking the deletion region.

Note: The phenotype of significantly larger or smaller deletions within this region may be clinically distinct from the 3q29 recurrent deletion (see Genetically Related Disorders).

Although several genes of interest (e.g., DLG1, FBXO45, PAK2, RNF168) are within the 1.6-Mb recurrent deletion, no single gene in which pathogenic variants are causative has been identified (see Molecular Genetics for genes of interest in the deleted region).

Genomic testing methods that determine the copy number of sequences can include chromosomal microarray (CMA) or targeted deletion analysis. Note: The 3q29 recurrent deletion cannot be identified by routine analysis of G-banded chromosomes or other conventional cytogenetic banding techniques.

  • Chromosomal microarray (CMA) using oligonucleotide arrays or SNP arrays can detect the recurrent deletion in a proband. The ability to size the deletion depends on the type of microarray used and the density of probes in the chr3:195998129-197623129 region.
    Note: (1) Most individuals with a 3q29 recurrent deletion are identified by CMA performed in the context of evaluation for developmental delay, intellectual disability, or autism spectrum disorder. (2) Prior to 2005 many CMA platforms did not include coverage for this region and thus may not have detected this deletion. This recurrent deletion was detected by early BAC arrays; at least 14 individuals with 3q29 deletion were identified with this technology [Ballif et al 2008].
  • Targeted deletion analysis. FISH analysis, quantitative PCR (qPCR), multiplex ligation-dependent probe amplification (MLPA), or other targeted quantitative methods may be used to test relatives of a proband known to have the 3q29 recurrent deletion.
    Note: (1) Targeted deletion testing is not appropriate for an individual in whom the 3q29 recurrent deletion was not detected by CMA designed to target chr3:195998129-197623129. (2) It is not possible to size the deletion routinely by use of targeted methods.

Table 1.

Genomic Testing Used in the 3q29 Recurrent Deletion

Deletion 1ClinGen ID 2Region Location 3, 4Test MethodTest Sensitivity
ProbandAt-risk family members
1.6-Mb heterozygous deletion at 3q29ISCA-37443GRCh37/hg19 chr3:195,756,054-197,344,665CMA 5100%100%
Targeted deletion analysis 6See footnote 7100% 8
1.

See Molecular Genetics for details of the deletion.

2.

Standardized clinical annotation and interpretation for genomic variants from the Clinical Genome Resource (ClinGen) project (formerly the International Standards for Cytogenomic Arrays (ISCA) Consortium)

3.

Genomic coordinates represent the minimum deletion size associated with the 3q29 recurrent deletion as designated by ClinGen. Deletion coordinates may vary slightly based on array design used by the testing laboratory. Note that the size of the deletion as calculated from these genomic positions may differ from the expected deletion size due to the presence of segmental duplications near breakpoints. The phenotype of significantly larger or smaller deletions within this region may be clinically distinct from the 3q29 recurrent deletion (see Genetically Related Disorders).

4.

See Molecular Genetics for genes of interest included in this region.

5.

Chromosomal microarray analysis (CMA) using oligonucleotide arrays or SNP arrays. CMA designs in current clinical use target the 3q29 region. Note: The 3q29 recurrent deletion may not have been detectable by older oligonucleotide or BAC platforms.

6.

Targeted deletion analysis methods can include: FISH, quantitative PCR (qPCR), and multiplex ligation-dependent probe amplification (MLPA) as well as other targeted quantitative methods.

7.

Not applicable. Targeted deletion analysis is not appropriate for an individual in whom the 3q29 recurrent deletion was not detected by CMA designed to target this region.

8.

Targeted deletion analysis may be used to test at-risk relatives of a proband known to have the 3q29 recurrent deletion.

Evaluating at-risk relatives. FISH, qPCR, or other quantitative methods of targeted deletion analysis can be used to identify the 3q29 recurrent deletion in at-risk relatives of the proband. Testing parental samples is important in determining recurrence risk (see Genetic Counseling).

Clinical Characteristics

Clinical Description

Global developmental delay and/or intellectual disability (ID) are common to almost all individuals with the 3q29 recurrent deletion. Aside from this, clinical presentation can vary. Although some facial dysmorphology has been noted – including a long narrow face, short philtrum, high nasal bridge, and large ears [Ballif et al 2008] – the facial phenotype is subtle and not specific.

The summary below is based on the comprehensive review of all reported cases in Cox & Butler [2015] and the self-reported findings in 44 individuals from the 3q29 deletion registry [Glassford et al 2016].

The following clinical manifestations have been reported in more than one individual with the recurrent deletion.

In the first year of life

  • Feeding problems (64%) and failure to gain weight (39%)
  • Jaundice (34%)
  • Hypotonia (34%) and hyporeflexia (7%)
  • Respiratory distress (25%) (although this may have to do with normal respiratory disease due to RSV, parainfluenza, influenza, or rhinovirus, and may not be related to the deletion)
  • Congenital heart defects including patent ductus arteriosus (12%), ventricular septal defect (5%), pulmonary valvar stenosis (5%)

Developmental delay. Specific data on developmental issues are limited. On average achievement of developmental milestones is delayed between six to twelve months (depending on the milestone). For example, walking is usually achieved at age 20 months (vs 12 months) and speaking single words at age 23 months (vs 12 months). Over time, children with the 3q29 deletion show a range of intellectual disability, with most having mild to moderate ID. Fewer than 5% have severe ID. Likewise, only one of 44 individuals reported to have the 3q29 deletion is completely nonverbal.

Learning problems

  • Speech delay (60%)
  • Receptive language delay (33%)
  • Verbal apraxia (a motor speech disorder) (19%)
  • Short-term memory problems (17%)
  • Visual processing deficits (12%)
  • Dysphasia/aphasia (10%)
  • Auditory processing disorder (7%)

Neuropsychiatric disorders (see Note)

  • Autism spectrum disorder (26%)
  • Anxiety disorder (19%)
  • Panic attacks (10%)
  • Schizophrenia (5%-40%)
  • Depression (at least 5%)
  • Bipolar disorder (5%)

Individuals with the 3q29 deletion may exhibit more than one neuropsychiatric disorder. For example, roughly 50% of individuals with 3q29 deletion and ASD also report an anxiety disorder.

Note: Data from neuropsychiatric phenotypes were obtained from 44 children, many of whom had not yet reached the age of risk for psychiatric phenotypes. Research in adults has established that the risk for schizophrenia is 40-fold increased [Mulle 2015, Mulle et al 2010]; the risk for bipolar disorder is also increased [Clayton-Smith et al 2010].

Recurrent ear infections (32%)

Gastrointestinal

  • Feeding problems in childhood (42%) sometimes necessitating feeding by gastrostomy tube
  • Gastroesophageal reflux disease (39%)
  • Chronic constipation (22%)
  • Dysphagia (12%)
  • Hiatal hernia (5%)
  • Chronic diarrhea (5%)

Dental

  • Dental caries (24%), weak or soft tooth enamel (19%), enamel hypoplasia (10%)
  • Abnormal dental spacing: crowded teeth (24%); widely spaced teeth (17%), large gap between central incisors (12%)
  • Abnormal tooth size: large (10%), small (7%)
  • Missing teeth (5%)

Genotype-Phenotype Correlations

No genotype-phenotype correlations for the 3q29 recurrent deletion are known.

Penetrance

Penetrance for the 3q29 recurrent deletion is not known. Reports of the deletion having been inherited from an unaffected parent suggest that while penetrance is high, it is likely not 100%.

It is unknown if penetrance differs in males and females.

Nomenclature

The 3q29 recurrent deletion may also be referred to as the “3q29 microdeletion syndrome” or the “3q29 deletion syndrome.”

Prevalence

The approximate prevalence is 1:30,000-1:40,000, based on a large population-based study in Iceland in which three of 101,655 individuals tested had the 3q29 recurrent deletion [Stefansson et al 2014]. Prevalence in other populations is not known.

Differential Diagnosis

The differential diagnosis of the 3q29 recurrent deletion is broad due to the variable spectrum and presence of relatively common abnormal phenotypes that occur in affected individuals including developmental delay, learning problems, and neuropsychiatric disorders. All manifestations of the 3q29 recurrent deletion can also be seen in individuals with other genomic disorders.

Management

Evaluations Following Initial Diagnosis

To establish the extent of disease and needs of an individual diagnosed with the 3q29 recurrent deletion, the following evaluations should be considered:

  • Comprehensive developmental assessment including evaluation of cognitive, speech and language, motor, and social skills
  • Psychiatric evaluation in individuals with evidence of neuropsychiatric manifestations including autism spectrum disorder (ASD)
  • Assessment for feeding problems and nutrition; consultation with pediatric feeding specialists as needed
  • Early consultation with a pediatric dentist
  • Evaluation in infancy for evidence of congenital heart disease
  • Consultation with a pediatric otolaryngologist as needed for recurrent otitis media
  • Consultation with a clinical geneticist and/or genetic counselor

Treatment of Manifestations

The following measures are appropriate:

  • Early speech and language therapy to address speech delays
  • Physical therapy as necessary to address fine and gross motor delays
  • Individualized education program (IEP) for school-age children
  • Care by a child psychiatrist for anxiety disorder and/or other neuropsychiatric manifestations
  • Applied behavioral analysis or other treatment for manifestations of ASD
  • Feeding therapy (including nutrition assessment) with a pediatric feeding specialist or behavioral pediatric psychologist; consideration of gastronomy tube for severe feeding problems and continued failure to thrive
  • Routine management of dental caries, congenital heart defects, and recurrent ear infections

Surveillance

Continued assessment of:

  • Feeding and nutrition
  • Developmental milestones
  • Cognitive development
  • Possible psychiatric manifestations

Evaluation of Relatives at Risk

Parents and older and younger at-risk sibs of a proband should be tested for the 3q29 recurrent deletion. Parents or sibs may have the deletion, but with only mild or nonexistent developmental delay or intellectual disability. The average age at onset for schizophrenia is 20-25 years; thus, mildly affected individuals remain at risk for neuropsychiatric manifestations and would benefit from monitoring and clinical evaluation.

See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.

Therapies Under Investigation

Search ClinicalTrials.gov for access to information on clinical studies for a wide range of diseases and conditions.

Genetic Counseling

Genetic counseling is the process of providing individuals and families with information on the nature, inheritance, and implications of genetic disorders to help them make informed medical and personal decisions. The following section deals with genetic risk assessment and the use of family history and genetic testing to clarify genetic status for family members. This section is not meant to address all personal, cultural, or ethical issues that individuals may face or to substitute for consultation with a genetics professional. —ED.

Mode of Inheritance

The 3q29 recurrent deletion is inherited in an autosomal dominant manner. Although most deletions are de novo, inherited deletions have been reported [Cox & Butler 2015].

Risk to Family Members

Parents of a proband

Sibs of a proband. The risk to the sibs of the proband depends on the genetic status of the parents:

  • If the 3q29 recurrent deletion identified in the proband is not identified in one of the parents, the risk to sibs is low (<1%) but greater than that of the general population because of the possibility of parental germline mosaicism for the deletion.
  • If one of the parents has the 3q29 recurrent deletion, the risk to each sib of inheriting the deletion is 50%. However, it is not possible to reliably predict the phenotype of the individual.

Offspring of a proband. Offspring of an individual with the 3q29 recurrent deletion have a 50% chance of inheriting the deletion. However, the phenotypic spectrum varies widely even among family members [Digilio et al 2009, Li et al 2009].

Other family members. The risk to other family members depends on the genetic status of the proband’s parents: if a parent has the 3q29 recurrent deletion, his or her family members may also have the deletion.

Related Genetic Counseling Issues

See Management, Evaluation of Relatives at Risk for information on evaluating at-risk relatives for the purpose of early diagnosis and treatment.

Family planning

  • The optimal time for determination of genetic risk and discussion of the availability of prenatal testing is before pregnancy. Similarly, decisions about testing to determine the genetic status of at-risk asymptomatic family members are best made before pregnancy.
  • It is appropriate to offer genetic counseling (including discussion of potential risks to offspring and reproductive options) to young adults who are at risk of having a child with the 3q29 recurrent deletion.

DNA banking is the storage of DNA (typically extracted from white blood cells) for possible future use. Because it is likely that testing methodology and our understanding of genes, allelic variants, and diseases will improve in the future, consideration should be given to banking DNA of affected individuals.

Prenatal Testing and Preimplantation Genetic Diagnosis

Pregnancies known to be at increased risk for the 3q29 recurrent deletion. Once the 3q29 recurrent deletion has been identified in an affected family member, prenatal testing for a pregnancy at increased risk for the 3q29 recurrent deletion and preimplantation genetic diagnosis are possible options.

Prenatal testing using genomic testing that will detect the 3q29 recurrent deletion found in the proband may be offered when:

  • A parent has the recurrent deletion;
  • The parents do not have the recurrent deletion but have had a child with the 3q29 recurrent deletion. In this instance, the recurrence risk associated with the possibility of parental germline mosaicism or other predisposing genetic mechanisms is probably slightly greater than that of the general population (though still <1%).

Differences in perspective may exist among medical professionals and within families regarding the use of prenatal testing, particularly if the testing is being considered for the purpose of pregnancy termination rather than early diagnosis. Although most centers would consider decisions about prenatal testing to be the choice of the parents, discussion of these issues is appropriate.

Pregnancies not known to be at increased risk for 3q29 recurrent deletion. CMA performed in a pregnancy not known to be at increased risk may detect the 3q29 recurrent deletion.

Note: Regardless of whether a pregnancy is known or not known to be at increased risk for the 3q29 recurrent deletion, prenatal test results cannot reliably predict the phenotype.

Resources

GeneReviews staff has selected the following disease-specific and/or umbrella support organizations and/or registries for the benefit of individuals with this disorder and their families. GeneReviews is not responsible for the information provided by other organizations. For information on selection criteria, click here.

  • Chromosome Disorder Outreach (CDO)
    PO Box 724
    Boca Raton FL 33429-0724
    Phone: 561-395-4252 (Family Helpline)
    Email: info@chromodisorder.org
  • Unique: The Rare Chromosome Disorder Support Group
    G1 The Stables
    Station Road West
    Oxted Surrey RH8 9EE
    United Kingdom
    Phone: +44 (0) 1883 723356
    Email: info@rarechromo.org; rarechromo@aol.com
  • 3q29 Deletion Registry
    Rollins School of Public Health
    Emory University
    1518 Clifton Road
    Atlanta GA 30322
    Phone: 404-727-3042
    Email: jmulle@emory.edu

Molecular Genetics

Information in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED.

Table A.

3q29 Recurrent Deletion: Genes and Databases

GeneChromosome LocusProtein
Unknown3q29Not applicable

Data are compiled from the following standard references: gene from HGNC; chromosome locus, locus name, critical region, complementation group from OMIM; protein from UniProt. For a description of databases (Locus Specific, HGMD) to which links are provided, click here.

Table B.

OMIM Entries for 3q29 Recurrent Deletion (View All in OMIM)

609425CHROMOSOME 3q29 DELETION SYNDROME

Deletion mechanism. Deletion breakpoints are usually found in low-copy repeats (LCRs) that flank the 3q29 recurrent deletion region. Non-allelic homologous recombination (NAHR) occurs when LCRs flanking the region misalign during meiosis followed by unequal crossing over between the LCRs. This process can produce gametes with the recurrent deletion or the reciprocal recurrent duplication. Breakpoints of the 3q29 recurrent deletion lie within the flanking LCRs, suggesting that the deletion arises through NAHR.

Genes of interest in this region. It is not currently known which of the genes in the region is responsible for the phenotype. However, there are several genes of interest: DLG1, FBXO45, PAK2, and RNF168 are all implicated (but not proven) to be of interest for the neurodevelopmental and psychiatric phenotypes.

  • DLG1 plays a role in trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and N-methyl-D-aspartate (NMDA) receptors to the neuronal membrane.
  • FBXO45 is required for synapse formation, axon path finding, and neuronal migration.
  • PAK2 is involved in mediating molecular processes such as neuron migration, outgrowth, and spine morphogenesis, and also controls neuronal differentiation.
  • RNF168 is part of the cellular machinery responsible for the repair of DNA double-strand breaks. Pathogenic variants result in RIDDLE syndrome, which is characterized by immunodeficiency and intellectual disability [Stewart et al 2009].

References

Literature Cited

  1. Ballif BC, Theisen A, Coppinger J, Gowans GC, Hersh JH, Madan-Khetarpal S, Schmidt KR, Tervo R, Escobar LF, Friedrich CA, McDonald M, Campbell L, Ming JE, Zackai EH, Bejjani BA, Shaffer LG. Expanding the clinical phenotype of the 3q29 microdeletion syndrome and characterization of the reciprocal microduplication. Mol Cytogenet. 2008;1:8. [PMC free article: PMC2408925] [PubMed: 18471269]
  2. Clayton-Smith J, Giblin C, Smith RA, Dunn C, Willatt L. Familial 3q29 microdeletion syndrome providing further evidence of involvement of the 3q29 region in bipolar disorder. Clin Dysmorphol. 2010;19:128–32. [PubMed: 20453639]
  3. Cox DM, Butler MG. A clinical case report and literature review of the 3q29 microdeletion syndrome. Clin Dysmorphol. 2015;24:89–94. [PMC free article: PMC5125389] [PubMed: 25714563]
  4. Digilio MC, Bernardini L, Mingarelli R, Capolino R, Capalbo A, Giuffrida MG, Versacci P, Novelli A, Dallapiccola B. 3q29 Microdeletion: a mental retardation disorder unassociated with a recognizable phenotype in two mother-daughter pairs. Am J Med Genet A. 2009;149A:1777–81. [PubMed: 19610115]
  5. Glassford MR, Rosenfeld JA, Freedman AA, Zwick ME, Mulle JG., Unique Rare Chromosome Disorder Support Group. Novel features of 3q29 deletion syndrome: Results from the 3q29 registry. Am J Med Genet A. 2016;170A:999–1006. [PMC free article: PMC4849199] [PubMed: 26738761]
  6. Li F, Lisi EC, Wohler ES, Hamosh A, Batista DA. 3q29 interstitial microdeletion syndrome: an inherited case associated with cardiac defect and normal cognition. Eur J Med Genet. 2009;52:349–52. [PubMed: 19460468]
  7. Mulle JG. The 3q29 deletion confers >40-fold increase in risk for schizophrenia. Mol Psychiatry. 2015;20:1028–9. [PMC free article: PMC4546529] [PubMed: 26055425]
  8. Mulle JG, Dodd AF, McGrath JA, Wolyniec PS, Mitchell AA, Shetty AC, Sobreira NL, Valle D, Rudd MK, Satten G, Cutler DJ, Pulver AE, Warren ST. Microdeletions of 3q29 confer high risk for schizophrenia. Am J Hum Genet. 2010;87:229–36. [PMC free article: PMC2917706] [PubMed: 20691406]
  9. Petrin AL, Daack-Hirsch S, L'Heureux J, Murray JC. A case of 3q29 microdeletion syndrome involving oral cleft inherited from a nonaffected mosaic parent: molecular analysis and ethical implications. Cleft Palate Craniofac J. 2011 Mar;48(2):222–30. [PMC free article: PMC2964377] [PubMed: 20500065]
  10. Stefansson H, Meyer-Lindenberg A, Steinberg S, Magnusdottir B, Morgen K, Arnarsdottir S, Bjornsdottir G, Walters GB, Jonsdottir GA, Doyle OM, Tost H, Grimm O, Kristjansdottir S, Snorrason H, Davidsdottir SR, Gudmundsson LJ, Jonsson GF, Stefansdottir B, Helgadottir I, Haraldsson M, Jonsdottir B, Thygesen JH, Schwarz AJ, Didriksen M, Stensbøl TB, Brammer M, Kapur S, Halldorsson JG, Hreidarsson S, Saemundsen E, Sigurdsson E, Stefansson K. CNVs conferring risk of autism or schizophrenia affect cognition in controls. Nature. 2014;505:361–6. [PubMed: 24352232]
  11. Stewart GS, Panier S, Townsend K, Al-Hakim AK, Kolas NK, Miller ES, Nakada S, Ylanko J, Olivarius S, Mendez M, Oldreive C, Wildenhain J, Tagliaferro A, Pelletier L, Taubenheim N, Durandy A, Byrd PJ, Stankovic T, Taylor AM, Durocher D. The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell. 2009;136:420–34. [PubMed: 19203578]

Chapter Notes

Revision History

  • 22 September 2016 (bp) Review posted live
  • 30 November 2015 (jgm) Original submission
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