Simpson-Golabi-Behmel Syndrome via the GPC3 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
563 GPC3$680.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity
Because most causative GPC3 mutations are deletions of single or multiple exons, clinical sensitivity of GPC3 sequencing is expected to be low.  For example, Li et al. (2001) failed to identify any individuals with point mutations among a group of 45 patients.  Seven patients in this study were found to have deletions.  In another study, however, six individuals were found to have GPC3 point mutations among a cohort of 25 patients (Veugelers et al. Hum Mol Genet 9:1321-1328, 2000).  Of these 25 patients, ten had a clinical diagnosis of SGBS and the remaining were diagnosed with other overgrowth syndromes, or were classified as undiagnosed overgrowth.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 GPC3$990.00 81479 Add to Order
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Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Features
Simpson-Golabi-Behmel syndrome (SGBS, OMIM 312870) is characterized clinically by pre- and postnatal overgrowth, distinct craniofacial and skeletal findings, and variable mental retardation. Craniofacial findings include macrocephaly, down slanting palpebral fissures, ocular hypertelorism, epicanthal folds, broad and flat nasal bridge with short nose, low-set and posteriorly rotated ears, and large mouth and tongue. Skeletal and limb abnormalities include postaxial polydactyly of hands, syndactyly of the second and third fingers and toes, short and webbed neck, fusion of vertebrae, and pectus excavatum. Language delay is common and mental retardation varies from mild to severe, although individuals with normal intelligence have been reported. Structural CNS findings, including agenesis of the corpus callosum and Chiari malformation and hydrocephalus, have been reported (Young et al. Ped Neurol 34:139-142, 2006). Other findings include cardiac conduction defects, supernumerary nipples, and increased risk of embryonal tumors (Li et al. Am J Med Genet 102:161-168, 2001). Female carriers may exhibit some features of SGBS (see below) and skewed X inactivation has been reported to correlate with clinical features in females (Yano et al. Clin Genet doi:10.1111, 2010).
Simpson-Golabi-Behmel syndrome is inherited as an X linked recessive disorder with marked inter- and intrafamilial variable expression. Mutations in the GPC3 gene (OMIM 300037) were found to cause SGBS (Pilia et al. Nat Genet 12:241-247, 1996) and, to date, are the only known cause of this disorder. Penetrance in males is thought to be complete (James et al. GeneReviews, 2006). Penetrance in female carriers is unknown, although carriers can manifest some clinical features (Golabi and Rosen Am J Med Genet 17:345-348, 1984; Rodriguez-Criado Am J Med Genet 138A:272-277, 2005). Nearly fifty GPC3 mutations have been reported. The great majority of these mutations are deletions of one or more exons. Other mutation types include missense, nonsense and splicing defects that presumably result in loss of function. Gonadal mosaicism has been documented for GPC3 mutations (Pilia et al. 1996; Romanelli et al. Clin Genet 72:384-386, 2007).
Testing Strategy
The putative extracellular proteoglycan, glypican-3, is coded by exons 1-8 of the GPC3 gene located on chromosome Xq26. Testing is accomplished by amplifying each coding exon and ~10 bp of adjacent noncoding sequence, then determining the nucleotide sequence using standard dideoxy sequencing methods and a capillary electrophoresis instrument. This test will not reliably detect partial GPC3 gene deletions. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.
Indications for Test
A child with pre- and post-natal overgrowth and characteristic craniofacial and skeletal features.


Official Gene Symbol OMIM ID
GPC3 300037
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Simpson-Golabi-Behmel Syndrome 312870

Related Test

Perlman Syndrome via the DIS3L2 Gene


Genetic Counselors
  • Aaron James, (2006). "Simpson-Golabi-Behmel Syndrome."
  • Golabi, M., Rosen, L. (1984). "A new X-linked mental retardation-overgrowth syndrome." Am J Med Genet 17(1): 345-58. PubMed ID: 6538755
  • Li, M., (2001). "GPC3 mutation analysis in a spectrum of patients with overgrowth expands the phenotype of Simpson-Golabi-Behmel syndrome." Am J Med Genet 102(2): 161-8. PubMed ID: 11477610
  • Pilia, G., (1996). "Mutations in GPC3, a glypican gene, cause the Simpson-Golabi-Behmel overgrowth syndrome." Nat Genet 12(3): 241-7. PubMed ID: 8589713
  • Rodriguez-Criado, G., (2005). "Clinical and molecular studies on two further families with Simpson-Golabi-Behmel syndrome." Am J Med Genet A 138A(3): 272-7. PubMed ID: 16158429
  • Romanelli, V., (2007). "Germinal mosaicism in Simpson-Golabi-Behmel syndrome." Clin Genet 72(4): 384-6. PubMed ID: 17850639
  • Veugelers, M., (2000). "Mutational analysis of the GPC3/GPC4 glypican gene cluster on Xq26 in patients with Simpson-Golabi-Behmel syndrome: identification of loss-of-function mutations in the GPC3 gene." Hum Mol Genet 9(9): 1321-8. PubMed ID: 10814714
  • Yano, S., (2010). "Familial Simpson-Golabi-Behmel syndrome: studies of X-chromosome inactivation and clinical phenotypes in two female individuals with GPC3 mutations." Clin Genet. PubMed ID: 20950395
  • Young, E. L., (2006). "Expanding the clinical picture of Simpson-Golabi-Behmel syndrome." Pediatr Neurol 34(2): 139-42. PubMed ID: 16458828
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Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

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Ordering Options

myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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