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1q21.1 Microdeletion

, MD and , MD.

Author Information
, MD
Department of Pediatrics, Section on Medical Genetics
Wake Forest University School of Medicine
Winston-Salem, North Carolina
, MD
Department of Pediatrics, Section on Medical Genetics
Wake Forest University School of Medicine
Winston-Salem, North Carolina

Initial Posting: .


Clinical characteristics.

The 1q21.1 microdeletion itself does not appear to lead to a clinically recognizable syndrome as some persons with the deletion have no obvious clinical findings and others have variable findings that most commonly include microcephaly (50%); mild intellectual disability (30%); mildly dysmorphic facial features; and eye abnormalities (26%). Other findings can include cardiac defects, genitourinary anomalies, skeletal malformations, and seizures (~15%). Psychiatric and behavioral abnormalities can include autism spectrum disorders, attention deficit hyperactivity disorder, autistic features, and sleep disturbances.


The recurrent distal 1.35-Mb 1q21.1 microdeletion can be detected by any number of molecular methods that determine the copy number of sequences within the deleted region, including chromosomal microarray analysis (CMA) using BAC clones or oligonucleotides, or array-based heterozygosity testing with polymorphic DNA markers (i.e., SNPs).


Treatment of manifestations: Routine treatment of ophthalmologic, cardiac, and neurologic findings; speech, occupational, and physical therapies as appropriate; specialized learning programs to meet individual needs; antiepileptic drugs or antipsychotic medications as needed.

Surveillance: Routine pediatric care; routine developmental assessments; monitoring of specific identified medical issues.

Genetic counseling.

The recurrent distal 1.35-Mb 1q21.1 deletion is inherited in an autosomal dominant manner. Between 18% and 50% of deletions occur de novo. The microdeletion can be inherited from either parent; a parent with the microdeletion may show a normal phenotype or an abnormal phenotype that is similar to but usually less severe than that of their child. Recurrence risk for future pregnancies for parents who do not have the microdeletion is low (probably <1%) but greater than that of the general population because of the possibility of germline mosaicism.


Clinical Diagnosis

Because of the variability of the phenotypic features, the diagnosis of the 1q21.1 microdeletion is often made during chromosomal microarray analysis (CMA). Features that should prompt consideration of this diagnosis include:

  • Developmental delays
  • Mild-to-moderate intellectual disability
  • Mild dysmorphic facial features (frontal bossing, deep-set eyes, bulbous nose)
  • Microcephaly


Cytogenetic testing. The 1q21.1 microdeletion cannot be identified by routine analysis of G-banded chromosomes or other conventional cytogenetic banding techniques.

Molecular Genetic Testing

Critical region. The diagnosis of the 1q21.1 microdeletion is confirmed by the finding of a heterozygous 1.35-Mb microdeletion at chromosome 1q21.1 from position 145-146.35 Mb (NCBI Build 36).

There are three possible deletions involving this region (see Molecular Genetics). For this GeneReview the 1q21.1 microdeletion refers to the recurrent distal 1.35-Mb deletion in the 1q21.1 region. Thirty-nine of the 46 individuals presented in the literature with the recurrent 1.35-Mb deletion have clinical information regarding developmental delays, intellectual disability, and congenital anomalies [Brunetti-Pierri et al 2008, Mefford et al 2008].

Genes. At least eight genes listed in OMIM are included in the recurrent distal 1.35-Mb deletion in the 1q21.1 region: PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, and GPR89B. No single gene mutations are known to cause the 1q21.1 microdeletion phenotype.

Clinical testing

Deletion/duplication analysis. The recurrent distal 1.35-Mb 1q21.1 microdeletion can be detected by any number of molecular methods that determine the copy number of sequences within the deleted region. Both whole-genome and targeted approaches can be applied:

  • Deletion/duplication analysis. Most deletions are detected by chromosomal microarray analysis (CMA) performed as part of the evaluation of an individual with developmental delay, intellectual disability, dysmorphic features, or congenital anomalies. CMA using BAC clones or oligonucleotides or array-based heterozygosity testing with polymorphic DNA markers (i.e., SNPs) can detect the recurrent 1.35-Mb deletion in a proband. The ability to size the deletion depends on the type of microarray used and the density of probes in the 1q21.1 region.
  • Targeted deletion analysis. Targeting methods such as fluorescence in situ hybridization (FISH), quantitative polymerase chain reaction (qPCR), or multiplex ligation-dependent probe amplification (MLPA) can be used to interrogate the 1q21.1 region for the microdeletion if the deletion is suspected clinically, or to confirm the microdeletion after genomic microarray analysis. Targeted approaches can also be used to detect the deletion in relatives of the proband.

    The feasibility of sizing the microdeletion depends on the number and distribution of probes in the 1q21.1 region for any method used (CMA, quantitative PCR, MLPA). Sizing the microdeletion is important to confirm that it is the 1.35-Mb deletion and not another of the microdeletions known to occur in chromosome band 1q21.1 (see Molecular Genetics). It is not possible to size the microdeletion routinely using FISH.

Table 1.

Summary of Molecular Genetic Testing Used to Detect the Recurrent 1q21.1 Deletion

Chromosomal RegionTest MethodMutations DetectedMutation Detection Frequency by Test Method 1
1q21.1Deletion / duplication analysis 2Recurrent 1.35-Mb deletion 100%

The ability of the test method used to detect a deletion or duplication that is present in the indicated chromosomal region


Testing that identifies deletions/duplications not readily detectable by sequence analysis of genomic DNA; a variety of methods including quantitative PCR, long-range PCR, heterozygosity testing, multiplex ligation-dependent probe amplification (MLPA), or targeted array GH (gene/segment-specific) may be used. A genomic chromosomal microarray (CMA or array GH) analysis that detects deletions/duplications across the genome may also include this gene/segment.

Interpretation of test results

Deletion analysis. Depending on the initial test used for detection, validation of the 1.35-Mb deletion by an independent method may be warranted. If high-density genomic microarray platforms have been used for the identification of the microdeletion, validation of the microdeletion may not be necessary, as it is unlikely that more than 50-100 adjacent targets show an abnormal copy number by chance. Such high-density platforms are also likely to confirm the microdeletion length as 1.35 Mb.

Testing Strategy

To establish the diagnosis in a proband requires detection of the 1.35-Mb deletion at chromosome 1q21.1. Most microdeletions are detected by CMA performed as part of the evaluation of developmental delay, intellectual disability, dysmorphic features, or congenital anomalies.

Note: The deletion cannot be identified by routine chromosome analysis.

Prenatal diagnosis and preimplantation genetic diagnosis (PGD) for at-risk pregnancies require prior identification of the deletion in the proband and/or parent.

Clinical Characteristics

Clinical Description

Individuals with the 1q21.1 microdeletion may have a wide range of clinical manifestations. The most common findings include developmental delay and mildly dysmorphic facies. However, there is not a clinically recognizable syndrome, as a subset of persons with the deletion do not have obvious clinical findings.

Table 2.

Features Present in Persons with a 1q21.1 Microdeletion

>75%Variable/mild dysmorphic facial features
Mild-moderate developmental delay (includes speech and motor delays)
25%-50%Short stature
Eye abnormalities
Intellectual disability
10%-25%Failure to thrive
Cardiac abnormalities
Joint laxity
<10%Brain malformations
Sensorineural deafness
Genitourinary abnormalities
Autism/autistic features

Most of the clinical data summarized is from 39 individuals with developmental delays, intellectual disability, and/or congenital anomalies who were found to have distal 1q21.1 microdeletion using chromosomal microarray [Mefford et al 2008, Brunetti-Pierri et al 2008].

The majority of persons with a 1q21.1 microdeletion have developmental delay. Most delays are mild and may involve global or specific areas, particularly gross motor development. Some may also have generalized learning disabilities throughout life. Intellectual disability, usually mild, is seen in approximately 30% of affected individuals.

Dysmorphic craniofacial features are a common finding but are highly variable and therefore not easily recognizable. The facial features may include frontal bossing, deep-set eyes, epicanthal folds, prominent and/or large nasal bridge with bulbous tip, long philtrum, and highly arched palate. Microcephaly is described in approximately 50% of individuals with a 1q21.1 microdeletion.

Eye abnormalities are seen in 26% of individuals and may include strabismus, chorioretinal and iris colobomas, microphthalmia, hypermetropia, Duane anomaly, and various types of cataracts (e.g., congenital, nuclear pulverulent).

1q21.1 microdeletions involving GJA5 have previously been associated with cardiac defects, but the sizes of the deletions were not fully elucidated and may have involved additional genes [Christiansen et al 2004]. Three of 505 (0.6%) individuals with congenital heart disease were found to have a deletion involving GJA5; their cardiac defects included aortic coarctation, interrupted aortic arch-type A, and interrupted aortic arch-type B. Mefford et al [2008] reported individuals with patent ductus arteriosus, truncus arteriosus, ventricular and atrial septal defects, bicuspid aortic valve, dilation of ascending aorta, aortic insufficiency, coarctation of the aorta, and transposition of the great vessels in individuals with 1q21.1 deletions.

Genitourinary anomalies include vesicoureteral reflux, hydronephrosis, inguinal hernia, and cryptorchidism.

Skeletal malformations are variable and include joint laxity, brachydactyly with or without short distal phalanges, broad thumbs, clinodactyly of the fifth finger, club foot, small feet, pes planus, broad or duplicated/bifid great toes, overlapping or syndactyly of the toes, and polydactyly of the hands or feet.

Most affected individuals have a normal neurologic physical examination, but hypotonia may be present. Seizures (e.g., tonic-clonic, absence) are seen in approximately 15% and often begin during the first year of life. One individual did not have seizures but had an EEG abnormality with slow waves over the anterior and central areas of both hemispheres [Mefford et al 2008].

Brain malformations are also described, including hydrocephalus and agenesis of the corpus callosum.

Sensorineural hearing loss has been reported in two individuals.

Psychiatric and behavioral abnormalities may also be present and include autism spectrum disorders, attention deficit hyperactivity disorder (10%), autistic features (8%), and sleep disturbances. In addition, distal 1q21.1 microdeletions have been identified in 0.2%-0.6% of persons with schizophrenia [International Schizophrenia Consortium 2008, Stefansson et al 2008, Walsh et al 2008].

Genotype-Phenotype Correlations

No genotype-phenotype correlations are observed in those with the recurrent distal 1.35-Mb deletion in the 1q21.1 region.


Little information is available regarding penetrance of the 1.35-Mb deletion. Similar to several of the newly described microdeletions (e.g., 16p11.2, 15q13.3), the 1q21.1 microdeletion can be inherited from a parent with minimally abnormal or completely normal clinical findings. In addition, several relatives of probands with the same 1q21.1 microdeletion (e.g., siblings, cousins) have a normal phenotype or only mild manifestations [Christiansen et al 2004; Shaffer et al 2006; Brunetti-Pierri et al 2008; Mefford et al 2008; Author, personal observation]. This suggests that the 1q21.1 microdeletion has reduced penetrance and variable expressivity.


The frequency of the recurrent distal 1.35-Mb 1q21.1 microdeletion is approximately 0.2% (46/22,563) of individuals with developmental delays, intellectual disabilities and/or congenital anomalies evaluated by CMA [Brunetti-Pierri et al 2008, Mefford et al 2008].

Differential Diagnosis

The 22q11.2 microdeletion syndrome is the most common microdeletion syndrome and has several features that overlap with those seen in individuals with the recurrent distal 1.35-Mb 1q21.1 deletion: developmental delays, learning disabilities (though not in 1q21.1 microdeletions the predominant nonverbal learning disability seen in 22q11.2 microdeletions), intellectual disability, behavioral abnormalities, short stature, eye abnormalities, cardiac defects, and schizophrenia. However, persons with a distal 1.35-Mb 1q21.1 deletion do not have the typical facial characteristics seen in the 22q11.2 microdeletion syndrome. Brunet et al [2009] identified two individuals with 1q21.1 copy number abnormalities who had clinical findings suggestive of a 22q11.2 microdeletion. One individual (who was previously reported in Mefford et al [2008]) had a duplication of the region that is typically deleted in individuals with thrombocytopenia absent radius (TAR) syndrome and a microdeletion of distal 1.35-Mb 1q21.1 on the same chromosome; the other had a duplication of the TAR-associated region only.


Evaluations Following Initial Diagnosis

To establish the extent of disease and needs of an individual diagnosed with the recurrent distal 1.35-Mb deletion in the 1q21.1 region, the following evaluations should be considered:

  • Ophthalmologic examination
  • Cardiac evaluation
  • Brain imaging in individuals with microcephaly, macrocephaly, and/or neurologic findings
  • Renal ultrasound examination
  • Comprehensive developmental assessment
  • Psychiatric evaluation in individuals with evidence of mental illness
  • Discussion of results with a medical geneticist or genetic counselor

Treatment of Manifestations

The following are indicated:

  • Routine treatment of ophthalmologic, cardiac, neurologic findings
  • Speech, occupational, and physical therapies, as appropriate
  • Specialized learning programs to meet individual needs

No specific antiepileptic or antipsychotic medications are indicated


Appropriate surveillance includes:

  • Routine pediatric care
  • Routine developmental assessments
  • Monitoring of specific identified medical issues

Evaluation of Relatives at Risk

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

Therapies Under Investigation

Search 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 recurrent distal 1.35-Mb 1q21.1 deletion is inherited in an autosomal dominant manner, with 18%-50% of deletions occurring de novo.

Risk to Family Members

Parents of a proband

  • Mefford et al [2008] found that in 50% (7/14) of the probands for whom parental testing was possible, a parent also had the microdeletion. Therefore, the other 50% (7/14) of the probands had a de novo microdeletion. In another study [Brunetti-Pierri et al 2008], 82% (9/11) of probands had inherited the microdeletion, and in 18% (2/11) it was de novo. Note: In 4/15 probands the parental status was unknown.

    The microdeletion can be inherited from either parent, and it does not appear that the phenotypic severity varies with the parent of origin. A parent with a microdeletion may show an abnormal phenotype similar to their child but in general is less severely affected. In approximately 25% of instances in which the microdeletion is inherited, the parent has a normal phenotype.
  • Recurrence risk for future pregnancies for parents who do not have the microdeletion is low (probably <1%) but greater than that of the general population because parents may have (a) germline mosaicism OR (b) low-level somatic mosaicism that also includes the germline.

Sibs of a proband. Because parents who have the microdeletion can be clinically unaffected, the risk to the sibs of a proband depends on the deletion status of the parents:

  • If a parent has the microdeletion, each sib is at a 50% risk of inheriting the microdeletion. An affected sib may show findings similar to those of the proband but could also have a milder or more severe phenotype.
  • In the unlikely event that a parent has germline mosaicism for the 1.35-Mb deletion or a balanced structural chromosome rearrangement involving the 1q21.1 region, the risk to sibs is increased and depends on the specific chromosome rearrangement.

Offspring of a proband. Individuals who have the 1.35-Mb deletion are expected to have a 50% chance of transmitting the deletion to each child.

Other family members. The risk to other family members depends on their deletion status.

Related Genetic Counseling Issues

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 have or are at risk of having a child with the 1.35-Mb 1q21.1 microdeletion.

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, mutations, and diseases will improve in the future, consideration should be given to banking DNA of affected individuals.

Prenatal Testing

Prenatal testing may be offered to unaffected parents who have had a child with a 1.35-Mb 1q21.1 microdeletion because of the recurrence risk (probably <1%) associated with the possibility of germline mosaicism.

Prenatal testing is technically feasible. Preparations from fetal cells obtained by amniocentesis usually performed at about 15 to 18 weeks' gestation or CVS at approximately ten to 12 weeks' gestation can be analyzed using CMA or FISH in the manner described in Molecular Genetic Testing.

Note: Gestational age is expressed as menstrual weeks calculated either from the first day of the last normal menstrual period or by ultrasound measurements.

Preimplantation genetic diagnosis (PGD) may be an option for some families in which the disease-causing mutation has been identified.


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)
  • Unique: The Rare Chromosome Disorder Support Group
    G1 The Stables
    Station Road West
    Oxted Surrey RH8 9EE
    United Kingdom
    Phone: +44 (0) 1883 723356
  • Simons VIP Connect Registry
    An online community for individuals with small chromosome deletions or duplications (CNV's) and their families. Simons VIP Connect is currently recruiting for a new research study aimed to better understand the medical, cognitive and behavioral phenotype of individuals with certain CNV's.

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.

1q21.1 Microdeletion: Genes and Databases

Gene SymbolChromosomal LocusProtein Name
Not applicable1q21​.1Not applicable

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

Table B.

OMIM Entries for 1q21.1 Microdeletion (View All in OMIM)


Molecular Genetic Pathogenesis

Similar to other genomic disorders (e.g., deletions and reciprocal duplications of 22q11.2, 7q11.2, 15q11q13, 15q13.3, 16p11.2, 17q21.31), the breakpoints of the 1q21.1 microdeletion commonly occur within flanking segmental duplications. In all these cases, the flanking segmental duplications in direct orientation share a high degree of sequence identity, which predisposes to rearrangements by non-allelic homologous recombination (NAHR). NAHR occurs from misalignment of and subsequent recombination between the flanking segmental duplications. The result is a deletion and a duplication of the sequences between the flanking segments, which is 1.35 Mb in the case of 1q21.1 microdeletion [Emanuel & Shaikh 2001, Lupski & Stankiewicz 2005].

In the 1q21.1 region, there are four copies of segmental duplications in direct orientation, each with high sequence identify. These noncontiguous segmental duplication elements are termed BP1, BP2, BP3, and BP4, so named because they are recombination breakpoint hotspots for deletion and duplication of sequences between the BP elements [Mefford et al 2008].

At least eight genes listed in OMIM are included in distal 1q21.1 deletions: PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, and GPR89B. Mutations in no single gene are associated with 1q21.1 microdeletion syndrome, but haploinsufficiency of one or more of the deleted genes likely contributes to the phenotype.


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Suggested Reading

  1. Kirov G. The role of copy number variation in schizophrenia. Expert Rev Neurother. 2010;10:25–32. [PubMed: 20021318]
  2. Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA, Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA, Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, Eis PS, Schwartz S, Knight SJ, Eichler EE. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat Genet. 2006;38:1038–42. [PubMed: 16906162]

Chapter Notes

Revision History

  • 24 February 2011 (me) Review posted live
  • 30 November 2010 (che) Original submission
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    2q37 Microdeletion Syndrome
    Doherty ES, Lacbawan FL. GeneReviews®. 1993
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