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Resources for Genetics Professionals — Mosaicism

, MD, , MS, CGC, and , MD.

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Mosaicism is the occurrence within a single individual or tissue of two or more cell lines with a different genetic or chromosomal composition. Mosaicism may involve somatic cells, germline cells, and/or tumor cells.


How does mosaicism arise in an individual and/or tissue?

Mosaicism can arise through one of the following mechanisms:

  • A de novo postzygotic genetic alteration occurring in an embryo any time after the first cell division
  • A de novo genetic alteration occurring in an actively dividing cell throughout the life of an individual resulting in somatic, germline, and/or placental mosaicism
  • Inactivation of select genes on the X chromosome in cells with more than one X chromosome (e.g., 46,XX females; 47,XXY males)
  • Spontaneous postzygotic loss of a trisomic chromosome resulting in mosaic uniparental disomy
  • Spontaneous reversion of a germline genetic alteration in a dividing cell that eliminates a germline variant (i.e., revertant mosaicism)
  • Mosaic nullizygosity, a mosaic (or postzygotic) genetic alteration occurring in an actively dividing cell in trans with a germline pathogenic variant resulting in mosaic loss of the normal allele in a fraction of cells (e.g., SOLAMEN syndrome, neurofibromatosis type 1, tuberous sclerosis)

Why are mosaic disorders important to recognize?

What are the suggestive clinical and radiographic features of mosaic disorders?

Clinical features of mosaic disorders can include:

  • Growth abnormalities (e.g., asymmetric or focal growth abnormalities, segmental overgrowth, generalized overgrowth)
  • Brain overgrowth and cortical malformations (macrocephaly or megalencephaly, focal cortical dysplasia, hemimegalencephaly)
  • Skin pigmentary abnormalities (e.g., linear or whorled hyper- and/or hypopigmentation)
  • Asymmetric limb anomalies (e.g., macrodactyly, leg length discrepancy)
  • Benign and/or malignant tumors
  • Vascular malformations (e.g., venous, capillary, mixed) and/or lymphatic malformations

Note: Clinical features of mosaic disorders can result from a growth advantage of mutated cells in affected tissue.

Radiographic features of mosaic disorders include:

  • Body MRI findings. Vascular malformations, lymphatic malformations, asymmetric overgrowth of any of a wide variety of tissues (e.g., adipose, muscle, nerve)
  • Brain MRI findings. Diffuse or focal brain malformations including focal cortical dysplasia, hemimegalencephaly, and polymicrogyria
  • Skeletal imaging. Asymmetric bony overgrowth (e.g., leg length discrepancy)

What type of genetic disorders have an increased incidence of mosaic presentation?

Genetic disorders in which the phenotype only occurs in a mosaic form typically as a result of embryonic lethality of a non-mosaic pathogenic variant. Pathogenic variants that are incompatible with life when present in the germline may result in a non-lethal recognizable phenotype when they occur postzygotically (see Table 1).

Genetic disorders associated with genes with an increased risk of de novo variants (including somatic variants; see Table 2). Variants are more likely to occur in large genes and/or genes with an increased number of:

  • Introns/exons due to an increased risk of de novo splice site alterations;
  • Repeat sequences due to an increased risk of misalignment during DNA replication;
  • Methylated CpG dinucleotides due to an increased risk of CpG to TpG transitions.

Chromosome disorders including those caused by:

Genetic disorders caused by postzygotic methylation abnormalities (i.e., epigenetic mosaicism; see Table 4)

Genetic disorders caused by pathogenic variant(s) prone to somatic reversion. Somatic genetic changes that eliminate a germline pathogenic variant and result in a selective advantage to specific dividing cells (e.g., hematopoietic cells) include (see Table 5):

Table 1.

Mosaic Disorders Caused by Postzygotic De Novo Heterozygous Variants

GeneDisorderReported Pathogenic Variants 1Reference Sequences
AKT1 Proteus syndrome c.49G>A (p.Glu17Lys) NM_005163​.2
AKT3 Hemimegalencephaly & focal cortical dysplasia (OMIM 611223)c.49G>A (p.Glu17Lys) NM_005465​.7
FGFR1 Encephalocraniocutaneous lipomatosis c.1638C>A (p.Asn546Lys)
c.1966A>G (p.Lys656Glu)
FGFR3 Keratinocytic epidermal nevus syndrome 2c.742C>T (p.Arg248Cys) 3 NM_000142​.5
GNA11 Cutis marmorata telangiectatica congenita Multiple GNA11 activating variants reported incl:
c.547C>T (p.Arg183Cys)
c.626A>C (p.Gln209Leu)
Diffuse capillary malformation w/overgrowth 4c.547C>T (p.Arg183Cys)
Phakomatosis pigmentovascularis type V 5c.547C>T (p.Arg183Cys)
c.547C>A (p.Arg183Ser)
GNAQ Extensive dermal melanocytosis 5c.548G>A (p.Arg183Gln)
c.626A>C (p.Gln209Pro)
Phakomatosis pigmentovascularis type V 5c.548G>A (p.Arg183Gln)
Sturge-Weber syndrome (OMIM 185300)c.548G>A (p.Arg183Gln)
GNAS Fibrous dysplasia / McCune-Albright syndrome c.601C>T (p.Arg201Cys)
c.601C>G (p.Arg201Gly)
c.601C>A (p.Arg201Ser)
c.602G>A (p.Arg201His)
c.602G>T (p.Arg201Leu)
c.679C>A (p.Gln227Lys)
c.680A>T (p.Gln227Leu)
c.680A>G (p.Gln227Arg)
c.681G>T (p.Gln227His)
HRAS Cutaneous-skeletal hypophosphatemia syndrome 6c.37G>C (p.Gly13Arg) 7
c.182A>G (p.Gln61Arg)
Schimmelpenning-Feuerstein-Mims syndrome (OMIM 163200)c.37G>C (p.Gly13Arg) 7
KRAS Encephalocraniocutaneous lipomatosis c.35G>A (p.Gly12Asp)
c.38G>A (p.Gly13Asp)
c.57G>C (p.Leu19Phe)
c.436G>A (p.Ala146Thr)
c.437C>T (p.Ala146Val)
Keratinocytic epidermal nevus syndrome 8c.35G>A (p.Gly12Asp)
Oculoectodermal syndrome (OMIM 600268)c.38G>A (p.Gly13Asp)
c.57G>C (p.Leu19Phe)
c.437C>T (p.Ala146Val)
c.436G>A (p.Ala146Thr)
Schimmelpenning-Feuerstein-Mims syndrome (OMIM 163200)c.35G>A (p.Gly12Asp)
MTOR Focal cortical dysplasia (OMIM 607341)Multiple MTOR activating variants reported NM_004958​.4
NRAS Congenital melanocytic nevus syndrome (neurocutaneous melanosis) (OMIM 137550)c.181C>A (p.Gln61Lys)
c.182A>G (p.Gln61Arg)
Cutaneous-skeletal hypophosphatemia syndrome 6c.182A>G (p.Gln61Arg)
Schimmelpenning-Feuerstein-Mims syndrome (OMIM 163200)c.182A>G (p.Gln61Arg)
PIK3CA PIK3CA-related overgrowth spectrum Multiple PIK3CA activating variants reported
PIK3R2 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 (OMIM 603387)c. 1117G>A (p.Gly373Arg)
c.1126A>G (p. Lys376Glu)
RHOA Ectodermal dysplasia w/facial dysmorphism & acral, ocular, & brain anomalies (OMIM 618727)c.139G>A (p.Glu47Lys)
c.211C>T (p.Pro71Ser)

Only a small number of pathogenic variants have been identified as causative of the genetic disorders listed in Table 1; it is possible that additional variants could be disease causing.


Non-mosaic (germline) FGFR3 variant p.Arg248Cys is associated with thanatophoric dysplasia.


Non-mosaic (germline) HRAS variant p.Gly13Arg is associated with Costello syndrome.


Table 2.

Heritable Genetic Disorders that Frequently Occur in Mosaic Form

ADCY5 ADCY5 dyskinesia ADSomatic mosaicism reported in 43% of persons w/de novo ADCY5 pathogenic variant
AKT3 1MPPH syndrome; hemimegalencephaly; focal cortical dysplasiaADSomatic mosaicism for gain-of-function variants reported
AR Androgen insensitivity syndrome XLSomatic & maternal gonadal mosaicism reported
Osteogenesis imperfecta ADSomatic/gonadal mosaicism present in ~8% of asymptomatic parents
DCX DCX-related disorders XLMultiple affected males & females w/somatic mosaicism reported typically w/milder phenotype
DMD Duchenne muscular dystrophy (See Dystrophinopathies.)XLGonadal mosaicism reported in 12%-15% of mothers of affected males; 2 somatic mosaicism also reported
EBP X-linked chondrodysplasia punctate 2 XLTypically lethal in non-mosaic males w/germline variant
IKBKG Incontinentia pigmenti XLLethal in nonmosaic males w/germline variant
JAG1 3 Alagille syndrome ADSomatic/gonadal mosaicism is present in ~8% of asymptomatic parents.
MTOR Smith-Kingsmore syndrome (OMIM 616638)ADSomatic mosaicism; parental gonadal mosaicism reported 4
NF1 Neurofibromatosis 1 AD~6.5% have somatic mosaicism (calculated from incidence of 1:36,000); gonadal mosaicism also reported
NF2 Neurofibromatosis 2 AD25%-33% of persons w/de novo variant have somatic mosaicism; gonadal mosaicism is rare.
NIPBL 5Cornelia de Lange syndrome (CDLS)ADSomatic mosaicism reported in ~10%-15% of persons w/NIPBL-related CDLS
PAFAH1B1 PAFAH1B1-related lissencephaly/subcortical band heterotopia ADSomatic mosaicism reported in persons w/milder phenotype
PHOX2B Congenital central hypoventilation syndrome AD
AR 6
Somatic/gonadal mosaicism is present in 5%-25% of asymptomatic parents.
PIK3R2 7Bilateral perisylvian polymicrogyria; MPPH syndromeADSomatic & suspected gonadal mosaicism for gain-of-function variants identified
PORCN Focal dermal hypoplasia XLAll affected males & some affected females are mosaic.
RB1 Retinoblastoma ADParental gonadal mosaicism identified in >4% of families
SOX2 SOX2 disorder ADParental gonadal mosaicism identified in 4.5% of families
Tuberous sclerosis ADSomatic mosaicism in >1% of probands; gonadal mosaicism also reported
WDR45 Beta-propeller protein-associated neurodegeneration XLSomatic mosaicism reported in females & males; lethal in non-mosaic males w/germline variant

Although CCND2 is also associated with MPPH syndrome, currently only AKT3 and PIK3R2 pathogenic variants are reported to be frequently mosaic.


Although NOTCH2 is also associated with Alagille syndrome, only JAG1 pathogenic variants are frequently mosaic.


While additional genes have been associated with Cornelia de Lange syndrome, currently only NIPBL pathogenic variants are reported to be frequently mosaic.


Congenital central hypoventilation syndrome caused by biallelic reduced penetrance PHOX2B pathogenic variants has been reported in two families.


Table 3.

Chromosome Disorders that Frequently Occur in Mosaic Form

Chromosome LocusDisorderMechanismComment
chr7 Silver-Russell syndrome Maternal UPD 1Isodisomy, heterodisomy, & segmental UPD have been reported.
chr11Maternal UPD 1Isodisomy, heterodisomy
chr8Trisomy 8Chromosome duplicationMost often postzygotic nondisjunction. Non-mosaic trisomy 8 is typically lethal.
chr9Trisomy 9Chromosome duplicationNondisjunction during meiosis in gonadal cell w/postzygotic chromosome deletion or postzygotic nondisjunction in mitosis. Non-mosaic trisomy 9 is typically lethal.
11p15.5 Beckwith-Wiedemann syndrome Paternal UPD 1Postzygotic somatic recombination resulting in isodisomy
12pPallister-Killian syndrome (OMIM 601803)Chromosome short arm duplicationNondisjunction during meiosis typically in maternal gonadal cell resulting in tetrasomy 12p
chrXTurner syndrome 2Chromosome deletionNondisjunction of sex chromosomes in meiosis or mitosis. Large % may be mosaic; mosaicism can incl additional aneuploidy (e.g., 45,X / 47,XXX), sex chromosome deletions, &/or isodisomy.

Additional mechanisms are reported but are not often associated with mosaicism.


Table 4.

Disorders Associated with Epigenetic Mosaicism

Chromosome LocusDisorder(s)MechanismComment
11p15.5Beckwith-Wiedemann syndrome; isolated lateralized overgrowthHypermethylation of IC1 on maternal alleleMosaicism identified in majority of persons w/hypermethylation of IC1 1
LOM at IC2LOM can vary between sample types (e.g., skin, blood), & partial vs complete LOM can be present in same tissue type. 2
11p15.5Silver-Russell syndrome; isolated hemihypoplasiaHypomethylation of ICR1 on paternal alleleCause of mosaic hypomethylation is largely unknown; rarely, deletions near ICR1 on paternal allele result in mosaic ICR1 hypomethylation. 3
15q11.2-q13 Angelman syndrome Hypomethylation of IC on maternal alleleMosaic hypomethylation identified in ~1% of all persons 4; cause is unknown.
15q11.2-q13 Prader-Willi syndrome IC defect → maternal-only methylation pattern at 15q11.2-q13Mosaic methylation alteration is rare 5; cause is unknown.

IC = imprinting center; IC1 = imprinting center 1; IC2 = imprinting center 2; ICR1 = imprinting center region 1; LOM = loss of methylation; UPD = uniparental disomy


Incidence of mosaicism is calculated based on 3% of individuals with imprinting center (IC) defects, 10%-15% of whom have an identifiable IC deletion; >40% of those without an IC deletion are mosaic [Beygo et al 2019].


Forty-four of 51 individuals with PWS with an imprinting center defect had no imprinting center deletion identified; two of 44 had a mosaic methylation pattern identified [Buiting et al 2003].

Table 5.

Genetic Disorders with Reported Somatic Reversion of Disease-Causing Variant

ADA Adenosine deaminase deficiency AR
BLM Bloom syndrome AR
Junctional epidermolysis bullosa AR
DMD Duchenne muscular dystrophy (See Dystrophinopathies.)XL
FAH Tyrosinemia type I AR
Fanconi anemia AR
XL 2
IL2RG X-linked severe combined immunodeficiency XL
RPA1 Dyskeratosis congenita AD
RPS19 3 Diamond-Blackfan anemia AD
SAMD9 MIRAGE syndrome AD
SAMD9L SAMD9L ataxia-pancytopenia syndrome AD
WAS Wiskott-Aldrich syndrome XL

Although additional genes have been associated with Fanconi anemia, only those listed here are currently reported to have pathogenic variants that have undergone somatic reversion [Nicoletti et al 2020].


FANCA-, FANCC-, FANCD2-, and UBE2T-related Fanconi anemia are inherited in an autosomal recessive manner. FANCB-related Fanconi anemia is inherited in an X-linked manner.


Although additional genes have been associated with Diamond-Blackfan anemia, to date revertant mosaicism has only been reported for RPS19 pathogenic variants.

Molecular Genetic Testing for Mosaic Disorders

Approaches for the detection of mosaic single nucleotide variants can include targeted analysis, single-gene testing, use of a multigene panel, and more comprehensive genomic testing.

Note: (1) The methodology used for testing a suspected mosaic disorder must be designed to detect mosaic variants – that is, variants at a less than 50% allelic level. (2) The percentage of mutated cells with an identified pathogenic variant is likely variable across different tissue types; more than one sample (ideally from a lesional tissue) may be required for a molecular diagnosis. (3) Pathogenic variant(s) may not be identified in a peripheral blood sample; therefore, absence of a pathogenic variant in a peripheral blood sample is not sufficient to exclude the diagnosis. (4) Some individuals have variant allele frequencies less than 1%, which can be challenging (or impossible) to detect with some assays and require ultrasensitive approaches.

  • Targeted analysis for the known pathogenic variant (see Table 1) in DNA derived from the affected tissue or, in some instances, DNA derived from buccal cells or skin fibroblasts (whether visibly affected or not) can be performed. Note: While only a small number of pathogenic variants have been identified as causative of the genetic disorders listed in Table 1, it is possible that additional variants could be disease causing.
  • Single-gene testing for somatic mosaicism. Sequence analysis of DNA derived from the affected tissue or DNA derived from buccal cells or skin fibroblasts (whether visibly affected or not) may detect a pathogenic variant not detected in DNA isolated from blood. Note: (1) Sensitivity to detect low-level mosaicism of a somatic pathogenic variant is highest using massively parallel sequencing (i.e., next-generation sequencing). (2) Sanger sequencing lacks the sensitivity for the detection of low-level mosaic variants.
  • A multigene panel that includes the gene(s) of interest may be considered. Note: (1) The genes included in the panel and the diagnostic sensitivity of the testing used for each gene vary by laboratory and are likely to change over time. (2) Clinicians need to determine which multigene panel is most likely to identify the genetic cause of the condition while limiting identification of pathogenic variants in genes that do not explain the underlying phenotype. (3) Methods used in a panel may include sequence analysis, deletion/duplication analysis, and/or other non-sequencing-based tests. (4) Somatic mosaicism for a pathogenic variant may not be detected by all commercially available multigene panels due primarily to the inability to test tissues other than blood (e.g., skin fibroblasts, buccal cells) and/or technical limitations in detecting low-level mosaicism; thus, clinicians considering use of a multigene panel need to select a panel specifically optimized to detect mosaicism for the gene of interest.
    For an introduction to multigene panels click here. More detailed information for clinicians ordering genetic tests can be found here.
  • More comprehensive genomic testing (when available) including exome sequencing and genome sequencing may be considered. Such testing may provide or suggest a diagnosis not previously considered (e.g., a variant in a different gene or genes that results in a similar clinical presentation). Note: Standard-depth exome and genome sequencing (including low-pass genome sequencing) may lack the sensitivity needed to detect low-level mosaic variants.
    For an introduction to comprehensive genomic testing click here. More detailed information for clinicians ordering genomic testing can be found here.

Approaches for the detection of mosaic chromosome disorders can include karyotype, chromosomal microarray (CMA), FISH, and DNA analysis for uniparental disomy (UPD) (Table 3).

  • Karyotype may be used to detect large chromosome deletions/duplications or chromosomal aneuploidy. In those with suspected mosaicism, additional cells and/or sample types (e.g., skin fibroblasts) should be analyzed. Karyotype cannot identify UPD.
  • CMA uses oligonucleotide or SNP arrays to detect genome-wide large deletions/duplications that cannot be detected by sequence analysis, and small chromosome rearrangements that may not be detected by karyotype. The ability to determine the size of the deletion/duplication depends on the type of microarray used and the density of probes in the region of interest. CMA will typically detect the presence or absence of a chromosome region but not the location of that region in relationship to other chromosome regions. SNP array analysis will detect UPD resulting from isodisomy but cannot detect heterodisomy.
  • Fluorescence in situ hybridization (FISH) using probes targeting the region of interest may be used to detect chromosome deletions/duplications that are too small to identify on karyotype. Detection is limited by the probes selected. FISH cannot identify UPD.
  • DNA analysis for UPD should be considered first in those with suspected UPD to detect isodisomy and/or heterodisomy of the region of interest. UPD testing requires parental samples to be informative. UPD may not be detected if a low level of mosaicism occurs in the tissue sampled, and testing of other tissues (e.g., skin fibroblasts) should be considered.

Approaches for the detection of epigenetic mosaicism include DNA methylation studies (see Table 4) to detect parent-specific methylation pattern at the region of interest. A methylation alteration may not be detected if a low level of mosaicism occurs in the tissue sampled, and testing of other tissues (e.g., skin fibroblasts) should be considered.

Approaches for the detection of somatic reversion include the combination of single-gene testing and gene-targeted deletion/duplication analysis (see Table 5).

  • Single-gene testing. Sequence analysis of the gene of interest using DNA derived from non-hematopoietic tissue (e.g., skin fibroblasts) may be considered. A germline pathogenic variant may not be detectable in leukocytes in some individuals with somatically acquired loss of heterozygosity, which may occur in hematopoietic cells of individuals with a germline gain-of-function pathogenic variant associated with somatic reversion (see Table 5). Single-gene testing can be used to identify a germline gain-of-function variant and acquired loss-of-function variant in cis in a gene of interest.
  • Gene-targeted deletion/duplication analysis may be considered to detect a mosaic deletion such as a deletion of a pathogenic variant in dividing cells (e.g., hematopoietic cells). Methods used may include a range of techniques such as quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions.

Genetic Counseling for Mosaic Disorders

Table 6 provides a general overview of genetic counseling considerations for disorders associated with mosaicism. (Note: Information provided in this table represents a high-level view of selected genetic counseling issues and does not address risks that may be specific to a given disorder or genetic alternation.)

Table 6.

Genetic Counseling for Mosaic Disorders

Type of Genetic DisorderMosaicism-Related Genetic Counseling Considerations
Mosaic disorders due to postzygotic de novo heterozygous variants (See Table 1.)
  • All probands are expected to represent simplex cases (i.e., a single affected family member).
  • Given the somatic mutational mechanism of the phenotype, the recurrence risk to sibs would be expected to be as in the general population.
Heritable genetic disorders that frequently occur in mosaic form (See Table 2.)
  • A mosaic parent may have segmental findings, unusually mild manifestations, or no discernible physical findings.
  • The risk that a parent w/germline mosaicism will transmit the pathogenic variant to offspring is <50%, but if the pathogenic variant is transmitted it will be present in every cell in the child's body & the child may be much more severely affected.
Chromosome disorders that frequently occur in mosaic form (See Table 3.)In the absence of a predisposing genetic alternation in a parent (e.g., biallelic BUB1B pathogenic variants), recurrence risk to sibs is expected to be low.
Disorders associated w/epigenetic mosaicism (See Table 4.)
  • A predisposing genetic alternation in parental gonadal cells is rare (e.g., deletions near ICR1 on the paternal allele resulting in mosaic ICR1 hypomethylation in Silver-Russell syndrome).
  • Given the somatic mutational mechanism of the phenotype, the recurrence risk to sibs would be expected to be as in general population.
Disorders w/reported somatic reversion of pathogenic variant (See Table 5.)

ICR1 = imprinting center region 1

Revision History

  • 27 October 2022 (sw) Initial posting


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