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Amelogenesis Imperfecta via the AMELX Gene

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

Sequencing

Test Code TestIndividual Gene PriceCPT Code Copy CPT Codes
1596 AMELX$440.00 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
In one study, AMELX mutations were identified in 2 out of 39 clinical diagnosed AI families. Both families demonstrated X-linked inheritance (Chan et al. 2011). In another study, AMELX mutations were reported to account for ~23% of pathogenic mutations found in patients affected with AI among the six genes tested (AMELX, ENAM, MMP20, KLK4, FAM83H, and WDR72) (Wright et al. 2011).

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Deletion/Duplication Testing via aCGH

Test Code TestIndividual Gene PriceCPT Code Copy CPT Codes
600 AMELX$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity
Six gross deletions/duplications large enough to be detected by PreventionGenetics' aCGH have been reported in AMELX (Hobson et al. 2009; HU et al. 2012; Human Gene Mutation Database).

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Clinical Features
Amelogenesis imperfecta (AI) is a heterogeneous condition of enamel defects affecting both primary and permanent dentitions. Affected teeth are usually small, discolored, pitted or grooved, and prone to rapid wear and breakage. Based on clinical and radiographic features of the enamel defects as well as on the mode of inheritance pattern, AI has been divided into 14 different subtypes, which can be grouped into four major forms: hypoplastic, hypomaturation, hypocalcified, and hypomaturation-hypoplastic with taurodontism (Witkop et al. 1988). Hypoplastic AI shows reduced enamel volume with pits or grooves, but enamel is usually hard and translucent. Hypomaturation and hypocalcified AI have hypomineralized enamel with nearly normal matrix volume. Hypocalcified AI may present soft enamel which can be easily scraped away by attrition. Hypomaturation enamel is hard, but brittle and prone to breaking off. Hypomaturation-hypoplastic with taurodontism shows reduced, hypomineralized enamel with pits; in addition, molars or other teeth may present enlarged pulp chambers (Witkop et al. 1988; Crawford et al. 2007).

AI and AI-related syndromes are currently known to be caused by mutations in the following genes: AMELX (Aldred et al. 1992), DLX3 (Price et al. 1998), ENAM (Mardh et al. 2002), KLK4 (Hart et al. 2004), MMP20 (Kim et al. 2005), FAM83H (Lee et al. 2008; Kim et al. 2008), WDR72 (El-Sayed et al. 2009), FAM20A (O'Sullivan et al. 2011), C4orf26 (Parry et al. 2012), ROGDI (Schossig et al. 2012), SLC24A4 (Parry et al. 2013), ITGB6 (Poulter et al. 2013; Wang et al. 2013), LAMB3 (Kim et al. 2013), CNNM4 (Parry et al. 2009) and NHS (Burdon et al. 2003).

Enamel defects can also occur as syndrome disorders. For example, Kohlschütter–Tönz syndrome features enamel defects, psychomotor delay or regression and seizures caused by ROGDI mutations (Tucci et al. 2013); Nance-Horan syndrome (NHS) is characterized by congenital cataracts, dental anomalies, dysmorphic features and mental retardation caused by mutations in the NHS gene (Burdon et al. 2003); Jalili Syndrome features autosomal-Recessive Cone-Rod dystrophy and amelogenesis Imperfecta caused by mutations in the CNNM4 gene (Parry et al. 2009); and mutations in the FAM20A gene cause amelogenesis imperfecta and gingival hyperplasia syndrome as well as amelogenesis imperfecta and renal syndrome (O’Sullivan et al. 2011; Wang et al. 2013).
Genetics
Mutations in the AMELX gene cause X-linked hypoplastic and /or hypomaturation amelogenesis imperfecta. Males are predominantly affected, but heterozygous female carriers may develop enamel defects. Clinical manifestations in females appear to be largely determined by random X-inactivation. The amelogenin coded by the AMELX gene is the major protein of enamel organic matrix and plays a key role in enamel structure and mineralization. To date, more than 20 unique pathogenic variants have been documented. They are missense (6/22), nonsense (2/22), small deletions (8/22), and large deletions involving the AMELX gene (6/22) (Chan et al., 2011; Wright et al. 2011; Hu et al. 2012; Human Gene Mutation Database). A large heterozygous deletion involving AMELX was reported in a female patient affected with microphthalmia with linear skin defects and amelogenesis imperfecta (Hobson et al. 2009).
Testing Strategy
Amelogenin protein is coded by exons 2 to 7 of the AMELX gene on chromosome Xp22.31-p22.1. Testing involves PCR amplification from genomic DNA and bidirectional Sanger sequencing of the coding exons and ~20bp of adjacent noncoding sequences. 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
Candidates for this test are patients with symptoms consistent with X-linked hypoplastic/hypomaturation amelogenesis imperfecta and the family members of patients who have known AMELX mutations.

Gene

Official Gene Symbol OMIM ID
AMELX 300391
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Amelogenesis Imperfecta, Type Ie 301200

Related Tests

Name
Amelogenesis Imperfecta via the C4orf26 Gene
Amelogenesis Imperfecta via the DLX3 Gene
Amelogenesis Imperfecta via the ENAM Gene
Amelogenesis Imperfecta via the FAM83H Gene
Amelogenesis Imperfecta via the KLK4 Gene
Amelogenesis Imperfecta via the MMP20 Gene
Amelogenesis Imperfecta via the WDR72 Gene
Epidermolysis Bullosa with Pyloric Atresia via the ITGA6 Gene
Junctional Epidermolysis Bullosa via the LAMB3 Gene
Kohlschutter-Tonz syndrome (KTS) via the ROGDI Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Aldred MJ, Crawford PJ, Roberts E, Thomas NS. 1992. Identification of a nonsense mutation in the amelogenin gene (AMELX) in a family with X-linked amelogenesis imperfecta (AIH1). Hum. Genet. 90: 413–416. PubMed ID: 1483698
  • Burdon KP, McKay JD, Sale MM, Russell-Eggitt IM, Mackey DA, Wirth MG, Elder JE, Nicoll A, Clarke MP, FitzGerald LM, Stankovich JM, Shaw MA, et al. 2003. Mutations in a Novel Gene, NHS, Cause the Pleiotropic Effects of Nance-Horan Syndrome, Including Severe Congenital Cataract, Dental Anomalies, and Mental Retardation. Am J Hum Genet 73: 1120–1130. PubMed ID: 14564667
  • Chan H-C, Estrella NMRP, Milkovich RN, Kim J-W, Simmer JP, Hu JC-C. 2011. Target gene analyses of 39 amelogenesis imperfecta kindreds: AI mutations. European Journal of Oral Sciences 119: 311–323. PubMed ID: 22243262
  • Crawford PJ, Aldred M, Bloch-Zupan A. 2007. Amelogenesis imperfecta. Orphanet Journal of Rare Diseases 2: 17. PubMed ID: 17408482
  • El-Sayed W, Parry DA, Shore RC, Ahmed M, Jafri H, Rashid Y, Al-Bahlani S, Harasi S Al, Kirkham J, Inglehearn CF, Mighell AJ. 2009. Mutations in the Beta Propeller WDR72 Cause Autosomal-Recessive Hypomaturation Amelogenesis Imperfecta. The American Journal of Human Genetics 85: 699–705. PubMed ID: 19853237
  • Hart PS. 2004. Mutation in kallikrein 4 causes autosomal recessive hypomaturation amelogenesis imperfecta. Journal of Medical Genetics 41: 545–549. PubMed ID: 15235027
  • Hobson GM, Gibson CW, Aragon M, Yuan Z, Davis-Williams A, Banser L, Kirkham J, Brook AH. 2009. A Large X-Chromosomal Deletion is Associated with Microphthalmia with Linear Skin Defects (MLS) and Amelogenesis Imperfecta (XAI). Am J Med Genet A 149A: 1698–1705. PubMed ID: 19610109
  • Hobson GM, Gibson CW, Aragon M, Yuan Z, Davis-Williams A, Banser L, Kirkham J, Brook AH. 2009. A large X-chromosomal deletion is associated with microphthalmia with linear skin defects (MLS) and amelogenesis imperfecta (XAI). American Journal of Medical Genetics Part A 149A: 1698–1705. PubMed ID: 19610109
  • Hu JC-C, Chan H-C, Simmer SG, Seymen F, Richardson AS, Hu Y, Milkovich RN, Estrella NMRP, Yildirim M, Bayram M, Chen C-F, Simmer JP. 2012. Amelogenesis Imperfecta in Two Families with Defined AMELX Deletions in ARHGAP6. PLoS ONE 7: e52052. PubMed ID: 23251683
  • Human Gene Mutation Database (Bio-base).
  • Kim J, Simmer J, Hart T, Hart P, Ramaswami M, Bartlett J, Hu J. 2005. MMP-20 mutation in autosomal recessive pigmented hypomaturation amelogenesis imperfecta. J Med Genet 42: 271–275. PubMed ID: 15744043
  • Kim J-W, Lee S-K, Lee ZH, Park J-C, Lee K-E, Lee M-H, Park J-T, Seo B-M, Hu JC-C, Simmer JP. 2008. FAM83H Mutations in Families with Autosomal-Dominant Hypocalcified Amelogenesis Imperfecta. The American Journal of Human Genetics 82: 489–494. PubMed ID: 18252228
  • Kim JW, Seymen F, Lee KE, Ko J, Yildirim M, Tuna EB, Gencay K, Shin TJ, Kyun HK, Simmer JP, Hu JC-C. 2013. LAMB3 mutations causing autosomal-dominant amelogenesis imperfecta. J. Dent. Res. 92: 899–904. PubMed ID: 23958762
  • Lee S-K, Hu JC-C, Bartlett JD, Lee K-E, Lin BP-J, Simmer JP, Kim J-W. 2008. Mutational Spectrum of FAM83H: The C-Terminal Portion is Required for Tooth Enamel Calcification. Hum Mutat 29: E95–E99. PubMed ID: 18484629
  • Mårdh CK, Bäckman B, Holmgren G, Hu JC-C, Simmer JP, Forsman-Semb K. 2002. A nonsense mutation in the enamelin gene causes local hypoplastic autosomal dominant amelogenesis imperfecta (AIH2). Hum. Mol. Genet. 11: 1069–1074. PubMed ID: 11978766
  • O’Sullivan J, Bitu CC, Daly SB, Urquhart JE, Barron MJ, Bhaskar SS, Martelli-Junior H, Santos Neto PE dos, Mansilla MA, Murray JC, Coletta RD, Black GCM, et al. 2011. Whole-Exome Sequencing Identifies FAM20A Mutations as a Cause of Amelogenesis Imperfecta and Gingival Hyperplasia Syndrome. Am J Hum Genet 88: 616–620. PubMed ID: 21549343
  • Parry DA, Brookes SJ, Logan CV, Poulter JA, El-Sayed W, Al-Bahlani S, Harasi S Al, Sayed J, Raïf EM, Shore RC, Dashash M, Barron M, et al. 2012. Mutations in C4orf26, Encoding a Peptide with In Vitro Hydroxyapatite Crystal Nucleation and Growth Activity, Cause Amelogenesis Imperfecta. The American Journal of Human Genetics 91: 565–571. PubMed ID: 22901946
  • Parry DA, Mighell AJ, El-Sayed W, Shore RC, Jalili IK, Dollfus H, Bloch-Zupan A, Carlos R, Carr IM, Downey LM, Blain KM, Mansfield DC, et al. 2009. Mutations in CNNM4 Cause Jalili Syndrome, Consisting of Autosomal-Recessive Cone-Rod Dystrophy and Amelogenesis Imperfecta. Am J Hum Genet 84: 266–273. PubMed ID: 19200525
  • Parry DA, Poulter JA, Logan CV, Brookes SJ, Jafri H, Ferguson CH, Anwari BM, Rashid Y, Zhao H, Johnson CA, Inglehearn CF, Mighell AJ. 2013. Identification of Mutations in SLC24A4, Encoding a Potassium-Dependent Sodium/Calcium Exchanger, as a Cause of Amelogenesis Imperfecta. The American Journal of Human Genetics 92: 307–312. PubMed ID: 23375655
  • Poulter JA, Brookes SJ, Shore RC, Smith CEL, Farraj L Abi, Kirkham J, Inglehearn CF, Mighell AJ. 2013. A missense mutation in ITGB6 causes pitted hypomineralized amelogenesis imperfecta. Human Molecular Genetics. PubMed ID: 24319098
  • Price JA, Wright JT, Kula K, Bowden DW, Hart TC. 1998. A common DLX3 gene mutation is responsible for tricho-dento-osseous syndrome in Virginia and North Carolina families. J Med Genet 35: 825–828. PubMed ID: 9783705
  • Schossig A, Wolf NI, Fischer C, Fischer M, Stocker G, Pabinger S, Dander A, Steiner B, Tonz O, Kotzot D, Haberlandt E, Amberger A, et al. 2012. Mutations in ROGDI Cause Kohlschütter-Tönz Syndrome. Am J Hum Genet 90: 701–707. PubMed ID: 22424600
  • Tucci A, Kara E, Schossig A, Wolf NI, Plagnol V, Fawcett K, Paisán-Ruiz C, Moore M, Hernandez D, Musumeci S. 2013. Kohlschütter–Tönz Syndrome: Mutations in ROGDI and Evidence of Genetic Heterogeneity. Human mutation 34: 296–300. PubMed ID: 23086778
  • Wang S-K, Choi M, Richardson AS, Reid BM, Lin BP, Wang SJ, Kim J-W, Simmer JP, Hu JC-C. 2013. ITGB6 loss-of-function mutations cause autosomal recessive amelogenesis imperfecta. Hum. Mol. Genet. ddt611. PubMed ID: 24305999
  • Witkop CJ. 1988. Amelogenesis imperfecta, dentinogenesis imperfecta and dentin dysplasia revisited: problems in classification. Journal of Oral Pathology & Medicine 17: 547–553. PubMed ID: 3150442
  • Wright JT, Torain M, Long K, Seow K, Crawford P, Aldred MJ, Hart PS, Hart TC. 2011. Amelogenesis Imperfecta: Genotype-Phenotype Studies in 71 Families. Cells Tissues Organs 194: 279–283. PubMed ID: 21597265
Order Kits
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.

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.

Order Kits

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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