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KANSL1-Related Intellectual Disability Syndrome

, MD, PhD and , MD, PhD.

Author Information

Initial Posting: ; Last Revision: January 10, 2013.


Clinical characteristics.

The KANSL1-related intellectual disability syndrome is characterized by developmental delay/intellectual disability, neonatal/childhood hypotonia, dysmorphisms, congenital malformations, and behavioral features. Global psychomotor developmental delay is noted in all individuals from an early age. The majority of individuals with the KANSL1-related intellectual disability syndrome function in the mild to moderate range of intellectual disability. Other findings include epilepsy (55%), congenital heart defects (39%), renal and urologic anomalies (37%), and cryptorchidism (71% of males). Behavior in most is described as friendly, amiable, and cooperative.


The syndrome can be caused by a 500- to 650-kb heterozygous deletion at chromosome 17q21.31 that includes KANSL1 or a heterozygous intragenic pathogenic variant in KANSL1. Note: The 17q21.31 microdeletion cannot be identified by routine analysis of G-banded chromosomes or other conventional cytogenetic banding techniques.


Treatment of manifestations: Physiotherapy for feeding problems and motor delay, speech therapy and other interventions to augment communication, educational programs directed to specific disabilities identified. Routine treatment of: epilepsy; scoliosis, hip dislocation, and positional deformities of the feet; cryptorchidism; cardiac, renal, and urologic problems.

Surveillance: Routine ophthalmologic examinations for hypermetropia and strabismus; monitoring for progressive spine deformities.

Genetic counseling.

The KANSL1-related intellectual disability syndrome, caused by a microdeletion or a pathogenic variant in KANSL1, is inherited in an autosomal dominant manner, but to date almost all cases result from a de novo deletion or KANSL1 pathogenic variant. Thus, most affected individuals represent simplex cases, i.e., a single occurrence in a family. The recurrence risk for future pregnancies is low (probably <1%) but greater than that of the general population because of the possibility of germline mosaicism in one of the parents. No individuals with KANSL1-related intellectual disability syndrome have been known to reproduce. Prenatal testing is technically feasible, but the likelihood of recurrence in families who have had an affected child is low.

GeneReview Scope

KANSL1-Related Intellectual Disability Syndrome: Included Disorders

For synonyms and outdated names see Nomenclature.


Clinical Diagnosis

The clinical spectrum of the KANSL1-related intellectual disability syndrome is variable. Besides developmental delay and intellectual disability, no single clinical feature is required to establish the diagnosis, although childhood hypotonia is a common feature, reported in almost all affected individuals.

Features that should prompt consideration of this diagnosis in an individual with developmental delay or intellectual disability include:

  • Delayed speech
  • Mild to moderate neonatal/childhood hypotonia
  • Normal growth
  • Epilepsy
  • Dysmorphic facial features (see Figure 1):
    • Abnormal hair color/texture
    • Broad forehead and/or high anterior hairline
    • Ptosis
    • Blepharophimosis
    • Upward slanting palpebral fissures
    • Epicanthal folds
    • Large/prominent ears
    • Bulbous nose or tubular nose
    • Everted vermilion of the lower lip
  • Heart anomalies
  • Renal/urologic anomalies
  • Hypermobility of the joints
  • Hypermetropia
  • Deformities of the feet and/or spine
  • Friendly/amiable disposition
Figure 1. . Photographs of eight different individuals with a 17q21.

Figure 1.

Photographs of eight different individuals with a 17q21.31 deletion


Cytogenetic testing. The 17q21.31 microdeletion cannot be identified by routine analysis of G-banded chromosomes or other conventional cytogenetic banding techniques.

Molecular Genetic Testing

Gene. KANSL1 is the only gene in which mutation is known to account for the majority of features of the syndrome [Koolen et al 2012b, Zollino et al 2012]

The KANSL1-related intellectual disability syndrome results from either of the following:

Clinical testing

Table 1.

Summary of Molecular Genetic Testing Used in KANSL1-Related Intellectual Disability Syndrome

Gene 1Test MethodVariants Detected 2Variant Detection Frequency by Test Method 3
KANSL1Deletion/duplication analysis 4, 5~600-kb deletion at 17q21.31 that includes KANSL1~95% 6
Sequence analysis 7Sequence variants~5% 6
Genotyping 8Not applicableNot applicable

See Molecular Genetics for information on allelic variants.


The ability of the test method used to detect a variant that is present in the indicated gene


Testing that identifies deletions/duplications not readily detectable by sequence analysis of the coding and flanking intronic regions of genomic DNA; included in the variety of methods that may be used are: quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and chromosomal microarray (CMA) that includes this gene/chromosome segment.


Methods may be genomic microarrays or targeted. BAC or oligonucleotide arrays or genotyping arrays can detect the common deletion in a proband. Targeted methods including fluorescence in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA) can be used if the syndrome is suspected clinically or for confirmation of the deletion after genomic microarray analysis. Targeted approaches can also be used for evaluating relatives of the proband for presence of the deletion.


The majority of affected individuals are identified by a genome-wide CMA screen for deletions/duplications. CMA using BAC, oligonucleotide, or SNP genotyping arrays can detect the deletion in a proband. The ability to size the deletion depends on the type of microarray used and the density of probes in the 17q21.3 region. It is too early to ascertain the frequency of the 17q21.31 microdeletion and a KANSL1 pathogenic variant. Given the fact that the chromosomal locus involved is flanked by segmental duplications, predisposing the locus to undergo deletion, it is likely that the recurrent microdeletion occurs more frequently.


Examples of pathogenic variants detected by sequence analysis may include small intragenic deletions/insertions and missense, nonsense, and splice site variants; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here. Note: Analysis of the genomic sequences can be difficult, as the mutant peak may be lower than expected because of the presence of low copy repeats in some individuals.


To date, testing in all unaffected parents from whom the deleted chromosome 17 originated has shown a 900-kb inversion involving chromosome 17q21.31. The frequency of this inversion (also referred to as the H2 lineage) in these parents is significantly greater than the ~20% frequency of the inversion found in the European population as a whole [Stefansson et al 2005] (p<10-5, Pearson’s Chi square test) [Koolen et al 2008]. Testing for the inversion is not routinely indicated (see Molecular Genetics).

Interpretation of test results

  • Deletion analysis. Depending on the initial test, validation of the deletion by an independent method may be warranted. If a high-density or targeted oligonucleotide genomic microarray platform that provides very dense coverage of the 17q21.31 region has been used for identification of the deletion, further validation may not be necessary, as it is unlikely that more than 50-100 adjacent DNA targets show an abnormal copy number by chance.

Testing Strategy

To establish the diagnosis in a proband requires detection of one of the following:

Most deletions are detected by genomic chromosomal microarray (CMA) analysis performed as part of the evaluation of developmental delay or intellectual disability.

If the KANSL1-related intellectual disability syndrome is suspected based on clinical features, a targeted technique such as FISH, MLPA, or quantitative PCR can be employed. See Table 1, footnote 4.

If a deletion is not identified, KANSL1 sequence analysis is recommended.

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

To evaluate at-risk relatives, targeted methods (FISH, MLPA, targeted [17q21.31 region-specific] CMA) or sequence analysis can be used to test for the 17q21.31 microdeletion or the KANSL1 sequence alteration, respectively.

Prenatal diagnosis and preimplantation genetic diagnosis (PGD) for at-risk pregnancies require prior identification of the deletion or pathogenic variant in the proband and/or of balanced carrier status in a parent (not reported to date).

Clinical Characteristics

Clinical Description

The KANSL1-related intellectual disability syndrome has a clinically recognizable phenotype that includes developmental delay/intellectual disability, neonatal/childhood hypotonia, dysmorphisms (Figure 1), congenital malformations and behavioral features (Table 2). Males and females are affected equally.

Table 2.

Features of KANSL1-Related Intellectual Disability Syndrome

Frequency 1Features
Very common (>75% of individuals)Distinctive facial features (see Clinical Diagnosis)
Developmental delay/ intellectual disability
Hypotonia (childhood)
Friendly/amiable disposition
Common (50%-75%)Epilepsy
Multiple nevi and other pigmentary skin and hair abnormalities
Nasal speech
Narrow/high palate
Dental anomalies
Slender/long fingers
Joint hypermobility and/or joint dislocation/dysplasia
Structural CNS anomalies
Renal & urogenital anomalies
Less common (25%-50%)Heart defects
Narrow hands
Hypoplasia hand muscles
Hip dislocation/ dysplasia
Persistence of fingertip pads
Slender lower limbs
Positional deformity of the feet
Scoliosis/ kyphosis
Occasional (10%-25%)Hearing loss due to chronic otitis media
Low birth weight
Short stature
Abnormal head shape 2
Pectus excavatum
Infrequent (<10%)Cleft lip/palate
Pyloric stenosis
Fused vertebrae

Abnormal head shape may include craniosynostosis

Global psychomotor developmental delay is noted in all individuals from an early age. The level of developmental delay varies significantly. The majority of individuals with the KANSL1-related intellectual disability syndrome function in the mild to moderate range of intellectual disability. Speech and language development seem to be particularly affected. Expressive language appears to be more severely affected than receptive language or motor skills.

Hypotonia with poor sucking and slow feeding can be evident in the neonatal period and during childhood. Feeding difficulties may require hospitalization and/or nasogastric tube feeding in some neonates.

Epilepsy including generalized seizures and unilateral clonic seizures is noted in 55%.

Growth. Short stature is not one of the most common clinical features of the syndrome. However, El Chehadeh-Djebbar et al reported on a child with a 17q21.31 microdeletion, short stature (-4 SD) and complete growth hormone deficiency and gonadotropic deficiency [El Chehadeh-Djebbar et al 2011]. Brain MRI showed partial pituitary stalk interruption, expanding the phenotypic spectrum of the syndrome.

Dysmorphic craniofacial features present in more than half of affected individuals include a broad forehead and/or high anterior hairline, long face, upward slanting palpebral fissures, epicanthic folds, a bulbous nose or tubular nose, large prominent ears, everted vermilion of the lower lip, and abnormal hair pigmentation and texture. The nose can have a high nasal bridge, a broad nasal root, long columella, and underdeveloped and/or thick alae nasi. The facial characteristics change with age. In infancy the facial gestalt is mostly characterized by hypotonia with an open mouth appearance. With increasing age there is usually elongation of the face and broadening of the chin, and the ‘‘tubular’’ or ‘‘pear’’ shape form of the nose may become more apparent.

Other common findings include dental anomalies, slender long fingers, persistence of the fetal fingertip pads, hypoplasia of the hand muscles, slender lower limbs, joint hypermobility, hip dislocation, and positional deformities of the feet. In addition, multiple nevi, other pigmentary skin abnormalities, and hair abnormalities have been reported [Koolen et al 2008, Tan et al 2009, Wright et al 2011].

Congenital heart defects are found in 39%. These are mainly septal heart defects, both atrial septal defects (ASD) and ventricular septal defects (VSD); however, cardiac valve disease, aortic root dilatation, and pulmonary stenosis have also been described.

Renal and urologic anomalies, including vesicoureteral reflux, hydronephrosis, pyelectasis, and duplex renal system, are found in 37%. Cryptorchidism has been reported in 71% of males.

Scoliosis is the most commonly observed spine anomaly; lordosis and kyphosis have also been reported and sometimes require surgery [Koolen et al 2008, Tan et al 2009].

Ophthalmologic abnormalities include strabismus and hypermetropia in 33%.

Behavior. In the vast majority of individuals, behavior is described as friendly, amiable, and cooperative, with or without frequent laughing. However, behavioral problems, including ADHD, have been reported [Koolen et al 2008, Tan et al 2009].

Life span. Longitudinal data are insufficient to determine life expectancy.

Genotype-Phenotype Correlations

Genotype-phenotype correlations in KANSL1-related intellectual disability syndrome have not been shown. Notably, the clinical features of children with the atypical deletions [Cooper et al 2011, Dubourg et al 2011, Kitsiou-Tzeli et al 2012, Koolen et al 2012b] and the pathogenic variants in KANSL1 [Koolen et al 2012b, Zollino et al 2012] are entirely in keeping with the phenotype seen in individuals with a classic 17q21.31 deletion.


Penetrance is 100%: clinical features of KANSL1-related intellectual disability syndrome are apparent in all individuals with the deletion or a KANSL1 pathogenic variant, although the extent and severity of clinical findings vary among individuals.


The disorder was first recognized following microarray analysis among large cohorts of unselected individuals with intellectual disability [Koolen et al 2006, Sharp et al 2006, Shaw-Smith et al 2006]. The identification of individuals with a similar phenotype and a de novo KANSL1 pathogenic variant [Koolen et al 2012b, Zollino et al 2012] led OMIM to assign the name Koolen syndrome to the condition.


The estimated frequency of the KANSL1-related intellectual disability syndrome is approximately on the order of 0.64% (95% CI, 0.35%-0.93%) of individuals with unexplained intellectual disability, indicating that the KANSL1-related intellectual disability syndrome is currently greatly underdiagnosed in individuals with intellectual disability [Koolen et al 2008]. Based on these numbers, the prevalence of the KANSL1-related intellectual disability syndrome in the population as a whole is estimated at approximately one in 16,000 individuals [Koolen et al 2008].

However, the frequency of 0.64% may be too high. Analysis of 15,767 DNA samples from children with a general diagnosis of intellectual disability and/or developmental delay revealed 23 children with 17q21.31 microdeletions (0.2%) [Cooper et al 2011].

The KANSL1-related intellectual disability syndrome occurs with equal frequency in males and females [Koolen et al 2008].

The discovery that heterozygous pathogenic variants in KANSL1 are sufficient to cause the KANSL1-related intellectual disability syndrome phenotype is recent; thus, reliable figures on the prevalence of any KANSL1 pathogenic variants are not yet available.

Differential Diagnosis

The most common findings in the KANSL1-related intellectual disability syndrome, developmental delay and childhood hypotonia, are common and relatively nonspecific indications for molecular cytogenetic analysis. However, the concurrent finding of characteristic facial dysmorphic features, epilepsy, hypermetropia, congenital heart defects, renal or urologic anomalies, cryptorchidism, and/or friendly/amiable behavior may prompt specific consideration of the diagnosis of KANSL1-related intellectual disability syndrome. Other diagnoses that may be considered in affected individuals include:

  • Deletion 22q11.2 (velocardiofacial syndrome) (VCFS). The KANSL1-related intellectual disability syndrome may be considered in patients who tested negative for deletion of 22q11.2. Developmental delay, long face, narrow palpebral fissures, prominent tubular nose, bulbous nasal tip, ventricular septal defects, and slender hands and digits are common clinical features in both syndromes.
  • Prader-Willi syndrome (PWS). Clinical features of the KANSL1-related intellectual disability syndrome that may also be seen with PWS include intellectual disability, severe neonatal/childhood hypotonia, seizures, global developmental delay, strabismus, upslanting palpebral fissures, cryptorchidism, and blonde to light brown hair. However, in contrast to PWS, childhood hyperphagia and central obesity have not been reported in the KANSL1-related intellectual disability syndrome, and behavioral problems and sleep disturbances are less common.
  • Fragile X syndrome. The face of adult males with the KANSL1-related intellectual disability syndrome may show some coarsening and elongation with increasing age, which may be similar to the facial gestalt of fragile X syndrome. The behavioral features, however, differ significantly.
  • Angelman syndrome. Varela et al [2006] described a girl with a 17q21.31 microdeletion and suggested a phenotypic resemblance to Angelman syndrome.
  • Cardiofaciocutaneous syndrome (CFC). Wright et al described four individuals with 17q21.31 microdeletions where previously the diagnosis of CFC syndrome was suggested [Wright et al 2011]. These individuals have a large number of nevi and other pigmentary skin abnormalities. These features, together with a coarse facial appearance, relative macrocephaly and significant learning disabilities, had led to the previous diagnostic suggestion of CFC syndrome in each of the four individuals.


Evaluations Following Initial Diagnosis

To establish the clinical consequences in an individual diagnosed with KANSL1-related intellectual disability syndrome, the following evaluations are recommended:

  • Multidisciplinary developmental evaluation, including feeding assessment
  • Comprehensive speech/language evaluation including audiologic examination
  • A renal ultrasound examination
  • Cardiac evaluation for possible heart anomalies including septal defect and aortic dilatation
  • Brain imaging studies in individuals with microcephaly and/or seizures
  • If seizures are suspected, EEG and consultation with a neurologist
  • Consideration of a Chiari malformation type 1 in individuals with the KANSL1-related intellectual disability syndrome presenting suggestive symptoms (headache, neck pain, cerebellar signs or muscle weakness) [Terrone et al 2012]
  • Investigation of growth hormone deficiency in individuals with KANSL1-related intellectual disability syndrome and short stature, defined by a height below - 2 SD scores for age and sex
  • Involvement of a clinical geneticist following the initial diagnosis

Treatment of Manifestations

Treatment includes the following:

  • Routine medical care by a pediatrician or other primary physician
  • Early intervention with physiotherapy for feeding problems and motor delay related to hypotonia. Physical therapy aimed at strengthening the muscles as well as therapy to improve development of the child's fine and gross motor skills may also be beneficial.
  • Speech therapy directed at improving verbal and nonverbal communication skills. Sign language, pictures, and computer touch screens may augment communication.
  • Educational programming directed to the specific disabilities identified
  • For epilepsy, treatment with routine antiepileptic drugs under the care of a neurologist. The seizures usually are easy to control with medication.
  • Orthopedic care as required for scoliosis, hip dislocation, and positional deformities of the feet
  • Standard treatment for cardiac, renal, urologic, and other medical issues
  • Treatment for cryptorchidism if indicated


The following are appropriate:

  • Ongoing pediatric care
  • Specialized neurologic care for individuals with epilepsy
  • Ophthalmologic examinations at routine intervals due to increased risk for hypermetropia and strabismus
  • Monitoring for spine deformities
  • Monitoring as needed of cardiac and renal/urologic abnormalities

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. Note: There may not be clinical trials for this disorder.

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 KANSL1-related intellectual disability syndrome, caused by a microdeletion at 17q21 or an intragenic KANSL1 pathogenic variant is inherited in an autosomal dominant manner, but almost all cases result from a de novo pathogenic variant.

Risk to Family Members

Parents of a proband

  • To date, all cases resulting from a KANSL1 pathogenic variant have been de novo.
  • To date, all microdeletions detected have been de novo, except for two families [Koolen et al 2012a]. The (phenotypically normal) mothers in both families were identified to have low-level somatic (and presumably gonadal) mosaicism [Koolen et al 2012a]. Thus, testing for mosaicism in the parents could be considered as a helpful tool in counseling, although gonadal mosaicism in one of the parents cannot be excluded.
  • Balanced chromosome rearrangements in parents have not been reported.

Sibs of a proband

  • The risk to the sibs of the proband depends on the genetic status of the parents.
  • When the parents are clinically unaffected, the risk to sibs is low (probably <1%) but greater than that of the general population because parents may have one of the following:

Offspring of a proband

  • Individuals who have the 17q21.31 deletion or a KANSL1 pathogenic variant have a 50% chance of transmitting the deletion/pathogenic variant to each child.
  • No individuals diagnosed with the KANSL1-related intellectual disability syndrome have been known to reproduce.

Other family members

  • The risk to other family members depends on the status of the proband's parents.
  • If a parent has a balanced chromosome rearrangement, his or her family members may be at risk.
  • No parent with a balanced chromosome rearrangement has been reported to date.

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.
  • It is appropriate to offer genetic counseling (including discussion of potential risks to offspring and reproductive options) to parents of a child with the KANSL1-related intellectual disability syndrome.

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

Prenatal testing may be offered to unaffected parents who have had a child with a 17q21.31 microdeletion or a KANSL1 pathogenic variant.

Prenatal testing is technically feasible. Chromosome preparations from fetal cells obtained by amniocentesis usually performed at approximately 15 to 18 weeks' gestation or CVS at approximately ten to 12 weeks' gestation can be analyzed for 17q21.31 microdeletions using FISH, MLPA, or CMA in the manner described in Molecular Genetic Testing. Intragenic KANSL1 pathogenic variants can be identified using DNA sequence analysis of KANSL1 (see 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 parents of a child with a 17q21.31microdeletion or a KANSL1 pathogenic variant.


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.

  • Supporting Families with Koolen-de Vries Syndrome
    Enriching lives through education, awareness and research.
    P.O. Box 470218
    Fort Worth TX 76147
    Phone: 833-721-KDVS
  • Chromosome Disorder Outreach (CDO)
    PO Box 724
    Boca Raton FL 33429-0724
    Phone: 561-395-4252 (Family Helpline)
  • Medline Plus
  • My46 Trait Profile
  • Unique: The Rare Chromosome Disorder Support Group
    G1 The Stables
    Station Road West
    Oxted Surrey RH8 9EE
    United Kingdom
    Phone: +44 (0) 1883 723356
  • GenIDA Registry: Genetically determined Intellectual Disabilities and Autism Spectrum Disorders
    A website for Patients, Families and Professionals

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.

KANSL1-Related Intellectual Disability Syndrome: Genes and Databases

GeneChromosome LocusProteinLocus-Specific DatabasesHGMDClinVar
KANSL117q21​.31KAT8 regulatory NSL complex subunit 1KANSL1 @ LOVDKANSL1KANSL1
Not applicable17q21​.31Not applicable

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

Table B.

OMIM Entries for KANSL1-Related Intellectual Disability Syndrome (View All in OMIM)


17q21.31 Microdeletion

Benign allelic variants. Within the Genome Reference Consortium Human genome build 37 (GRCh37) reference assembly, the 17q21.31 locus involved is defined approximately by chr17:43.4–44.8 Mbp. The locus encompasses ~600 kb of unique sequence and is flanked by extensive low-copy repeats (LCRs). Two haplotypes exist, in direct (H1) and inverted (H2) orientation [Stefansson et al 2005]. The H2 haplotype is enriched in Europeans, and carriers are predisposed to the 17q21.31 microdeletion [Koolen et al 2006, Sharp et al 2006, Koolen et al 2008, Zody et al 2008].

In every parent-child trio tested to date, the parent originating the deleted chromosome 17 carries at least one chromosome with H2 haplotype, which is significantly different from the approximately 20% frequency of the inversion in the European population reported by Stefansson et al (p<10-5, Pearson’s Chi square test) [Stefansson et al 2005, Koolen et al 2008]. The H2 haplotype results in a genomic structure with directly oriented LCR subunits that can undergo a deletion rearrangement via NAHR [Lupski 1998], suggesting that the inversion found in all parents of origin may be a necessary factor for the deletion to occur [Lupski 2006]. In the general population the H2 inversion is a risk factor for having offspring with a 17q21.31 microdeletion [Koolen et al 2008]. However, the frequency of de novo 17q21.31 microdeletions in carriers of the H2 inversion is low, and other as-yet poorly understood factors are likely to be important in the generation of the deletion.

Pathogenic allelic variants. The breakpoints of the 17q21.31 microdeletion were resolved with high through-put (next-generation sequencing) [Itsara et al 2012]. For two cases, breakpoints consistent with nonallelic homologous recombination involving only H2 chromosomal haplotypes, were observed. Molecular resolution revealed that the breakpoints occurred at different locations within a 145 kb LCR and disrupted KANSL1. In a third case, unequal crossover occurred interchromosomally between the H1 and H2 haplotypes and also this event was mediated by a homologous sequence [Itsara et al 2012].

Besides the recurrent classic 17q21.31 microdeletion, several atypical 17q21.31 deletions have been described in children with clinical features typically associated with the classic 17q21.31 microdeletion [Cooper et al 2011, Dubourg et al 2011, Kitsiou-Tzeli et al 2012, Koolen et al 2012b]. All these atypical deletions encompass at least KANSL1. Moreover, de novo pathogenic variants were identified in children with clinical features that are in keeping with the phenotype seen in individuals with a classic17q21.31 deletion, showing that KANSL1 is actually the gene involved in this microdeletion syndrome [Koolen et al 2012b, Zollino et al 2012].


Gene structure. There are several transcript variants of KANSL1 (Table A). The longest, NM_001193466.1, has 15 exons. For a detailed summary of gene and protein information, see Table A, Gene.

Pathogenic allelic variants. To date, de novo KANSL1 variants have been identified in at least six children with typical features of the KANSL1-related intellectual disability syndrome [Koolen et al 2012b, Zollino et al 2012, unpublished data]. All pathogenic variants result in or predict haploinsufficiency of KANSL1.

Table 3.

Selected KANSL1 Pathogenic Allelic Variants

DNA Nucleotide ChangeProtein Amino Acid ChangeReference Sequences
c.1652+1G>ASee footnote 1

Note on variant classification: Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.

Note on nomenclature: GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen​ See Quick Reference for an explanation of nomenclature.


Splice-site mutation resulting in skipping of exon 6, causing a frameshift and premature termination of the KANSL1 mRNA [Koolen et al 2012b]

Normal gene product. The longer KAT8 regulatory NSL complex subunit 1 isoform, NP_001180395.1, has 1105 amino acids. KANSL1 is a widely expressed gene encoding a member of the highly conserved nonspecific lethal (NSL) complex [Mendjan et al 2006]. This complex contains, among other proteins, the K (lysine) acetyltransferase KAT8, which influences gene expression through acetylation of histone H4K16 and the transcription factor p53 [Li et al 2009]. The NSL complex is recruited to target genes to facilitate activation of transcription in coordination with the histone H2K4 methyltransferase, MLL [Dou et al 2005].

Abnormal gene product. Interestingly, using whole transcriptome RNA-Seq, it was shown that genes that are differentially expressed in EBV-transformed cell lines from individuals with KANSL1-related intellectual disability syndrome and in those from controls are enriched in neuronal/synaptic processes, which is in line with the clinical phenotype [Koolen et al 2012b].


Literature Cited

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Chapter Notes


The authors gratefully acknowledge the members of 17q21.31 microdeletion support groups and other parents for their participation in research and for their generous sharing of information.

Revision History

  • 10 January 2013 (cd) Revision: sequence analysis of KANSL1 available clinically
  • 20 November 2012 (me) Comprehensive update posted live
  • 26 January 2010 (me) Review posted live
  • 28 August 2009 (dak) Original submission
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