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3-M Syndrome via the CCDC8 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
2882 CCDC8$580.00 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
Due to limited publications, clinical sensitivity is difficult to predict. The mutation detection rate by sequencing should be high because the three known unique pathogenic variants are missense, nonsense and a small deletion.

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Clinical Features
3-M syndrome is an intrauterine growth retardation disorder characterized by pre and postnatal growth retardation, a large head circumference, and a characteristic facial appearance including a prominent forehead, pointed triangular shaped face, a short upturned nose with anteverted nares, prominent mouth and lips and full eyebrows (van der Wal et al. 2001; Marik et al. 2002; Huber et al. 2005). Additional findings include a short broad neck, prominent trapezii, deformed sternum, short thorax, square shoulders, winged scapulae, hyperlordosis, short fifth fingers, slender long bones with diaphyseal constriction, tall vertebral bodies, delayed bone age and prominent heels (van der Wal et al. 2001; Huber et al. 2005; Huber et al. 2009). 3-M syndrome is currently known to be caused by pathogenic variants in the CUL7, OBSL1 and CCDC8 genes. CUL7 and OBSL1 are responsible for 77.5% and 16.3% of 3-M syndrome cases, respectively (AL-Dosari et al. 2012), while CCDC8 pathogenic variants were reported in only a few 3-M syndrome families (AL-Dosari et al. 2012; Hanson et al. 2011).
Genetics
3-M syndrome is an autosomal recessive disorder caused by pathogenic variants in the CUL7, OBSL1 and CCDC8 genes (Al-Dosari et al. 2012). The CCDC8 gene encodes the coiled-coil domain-containing protein, which partners with CUL7 and OBSL1 to form a 3-M complex to maintain microtubule and genome integrity (Yan et al. 2014). Only three unique CCDC8 pathogenic variants have been reported, and all three variants lead to premature protein termination c.84dupT (p.Lys29*); c.612dupG (p.Lys205Glufs*59) and c.803_807delAGATCinsT (p.Lys268Ilefs*40). The c.612dupG (p.Lys205Glufs*59) variant was found in four consanguineous South Asian 3-M families (Hanson et al. 2011).
Testing Strategy
The CCDC8 protein is coded by exon 1 of the CCDC8 gene on chromosome 19q13.32. Testing involves PCR amplification from genomic DNA and bidirectional Sanger sequencing of the coding exon and ~20 bp of adjacent noncoding sequences. We will also sequence any single portion (Test #100) or portions of this exon (Test #200) in family members of patients with a known mutation or to confirm research results.
Indications for Test
Candidates for this test are patients with symptoms consistent with 3-M syndrome, who do not have the CUL7 and OBSL1 pathogenic variants, and the family members of patients who have known CCDC8 mutations.

Gene

Official Gene Symbol OMIM ID
CCDC8 614145
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
3-M Syndrome 614205

Related Tests

Name
3-M Syndrome via the CUL7 Gene
Meier-Gorlin Syndrome Sequencing Panel
Meier-Gorlin Syndrome via the CDC6 Gene
Meier-Gorlin Syndrome via the CDT1 Gene
Meier-Gorlin Syndrome via the ORC1 Gene
Meier-Gorlin Syndrome via the ORC4 Gene
Meier-Gorlin Syndrome via the ORC6 Gene
Primordial Dwarfism via the POC1A Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Al-Dosari M.S. et al. 2012. The Journal of Pediatrics. 161: 139-45. PubMed ID: 22325252
  • Hanson D. et al. 2011. American Journal of Human Genetics. 89: 148-53. PubMed ID: 21737058
  • Huber C. et al. 2005. Nature Genetics. 37: 1119-24. PubMed ID: 16142236
  • Huber C. et al. 2009. European Journal of Human Genetics : Ejhg. 17: 395-400. PubMed ID: 19225462
  • Marik I. et al. 2002. Journal of Paediatrics and Child Health. 38: 419-22. PubMed ID: 12174011
  • Van der Wal G. et al. 2001. Clinical Dysmorphology. 10: 241–52. PubMed ID: 11665997
  • Yan J. et al. 2014. Molecular Cell. 54: 791-804. PubMed ID: 24793695
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TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  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 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 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 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

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 20 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.

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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.
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.

SPECIMEN TYPES
WHOLE BLOOD

(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.

DNA

(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.

CELL CULTURE

(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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