X-linked Lenz Microphthalmia Syndrome and Lethal Ogden Syndrome via the NAA10 Gene
Summary and Pricing
Test MethodExome Sequencing with CNV Detection
|Test Code||Test Copy Genes||Test CPT Code||Gene CPT Codes Copy CPT Codes||Base Price|
|8617||NAA10||81479||81479,81479||$890||Order Options and Pricing|
|Test Code||Test Copy Genes||Test CPT Code||Gene CPT Codes Copy CPT Code||Base Price|
|8617||NAA10||81479||81479(x2)||$890||Order Options and Pricing|
- Dana Talsness, PhD
Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).
Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).
The Sanger Sequencing method for this test is NY State approved.For Sanger Sequencing click here.
18 days on average for standard orders or 13 days on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
- Dana Talsness, PhD
Clinical Features and Genetics
Lenz microphthalmia syndrome (LMS) is a X-linked disorder characterized by unilateral or bilateral microphthalmia accompanied by multiple congenital extraocular abnormalities. Extraocular symptoms include developmental delay, skeletal abnormalities, genitourinary malformations, cleft lip and palate, digital anomalies, and anomalies of the ears and teeth. Mild to severe intellectual disability and seizures are seen in about 60% of affected males (Traboulsi et al. 1988; Esmailpour et al. 2014).
Ogden syndrome (OS) is an X-linked lethal disorder in infancy with severe developmental delays and a unique combination other symptoms including facial dysmorphic features, skin, skeletal, cardiac, genital and neurological abnormalities (Rope et al. 2011; Myklebust et al. 2015). X-chromosome inactivation was analyzed in heterozygous, affected OS women and all four women showed skewed X-inactivation (Myklebust et al. 2015).
Besides lethality, a distinct difference between MLS and OS is microphthalmia or anophthalmia, which only present in MLS. Reduced expressivity of the symptoms have been reported in female carriers (Rope et al. 2011; Esmailpour et al. 2014).
Hemizygous variants in NAA10 have been reported to be causative for allelic disorders LMS and OS. The mutation spectrum cannot be precisely described due to the limited number of documented cases. So far, only a missense (p.Ser37Pro) and a splice-site variant (c.471+2T>A) have been reported to be causative (Rope et al. 2011; Esmailpour et al. 2014). The splice-site variant in NAA10 has been shown to affect the retinoic acid signaling pathway that is is important for normal eye development and resulted in LMS. Whereas the missense variant was shown to reduce N-terminal acetyltransferase activity and resulted in severe phenotype OS (Rope et al. 2011; Esmailpour et al. 2014).
NAA10-encoded N-terminal acetyltransferase (NAT) is a ubiquitously expressed protein, which is involved in protein N-terminal acetylation (NTA). Recently, NAT has been shown to be involved in post-translational NTA, lysine acetylation, and NAT/KAT-independent functions (Dörfel and Lyon 2015). NTA is a commonly occurring protein modification in eukaryotes that has an important role in the modulation of protein-protein interaction, protein degradation, complex formation, subcellular targeting, and protein folding (Aksnes et al. 2015; Dörfel and Lyon 2015). NAT was also shown to be involved in the retinoic acid signaling pathway and normal eye development (Esmailpour et al. 2014).
LMS is genetically heterogeneous; NAA10 (MCOPS1 locus) and BCOR (MCOPS2 locus) are the only two genes so far identified (Ng 2014).
Clinical Sensitivity - Sequencing with CNV PGxome
Clinical sensitivity cannot be precisely estimated for Lenz microphthalmia and Ogden syndrome patients as they are rare disorders with a limited number of documented cases. Analytical sensitivity should be high because all NAA10 pathogenic variants reported are detectable by sequencing. No gross deletions or duplications have been reported so far (Human Gene Mutation Database).
This test provides full coverage of all coding exons of the NAA10 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).
Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).
Indications for Test
All patients with symptoms suggestive of MLS and OS are candidates.
All patients with symptoms suggestive of MLS and OS are candidates.
|Official Gene Symbol||OMIM ID|
- Aksnes H, Hole K, Arnesen T. 2015. Molecular, cellular, and physiological significance of N-terminal acetylation. Int Rev Cell Mol Biol 316: 267–305. PubMed ID: 25805127
- Dörfel MJ, Lyon GJ. 2015. The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 567: 103–131. PubMed ID: 25987439
- Esmailpour T, Riazifar H, Liu L, Donkervoort S, Huang VH, Madaan S, Shoucri BM, Busch A, Wu J, Towbin A, Chadwick RB, Sequeira A, Vawter MP, Sun G, Johnston JJ, Biesecker LG, Kawaguchi R, Sun H, Kimonis V, Huang T. 2014. A splice donor mutation in NAA10 results in the dysregulation of the retinoic acid signalling pathway and causes Lenz microphthalmia syndrome. Journal of Medical Genetics 51: 185–196. PubMed ID: 24431331
- Human Gene Mutation Database (Bio-base).
- Myklebust LM, Damme P Van, Stove SI, Dorfel MJ, Abboud A, Kalvik TV, Grauffel C, Jonckheere V, Wu Y, Swensen J, Kaasa H, Liszczak G, Marmorstein R, Reuter N, Lyon GJ, Gevaert K, Arnesen T. 2015. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Human Molecular Genetics 24: 1956–1976. PubMed ID: 25489052
- NG D. 2014. Lenz Microphthalmia Syndrome. GeneReviews™ [Internet]. Seattle (WA): University of Washington, Seattle. PubMed ID: 20301694
- Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ. 2011. Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency. The American Journal of Human Genetics 89: 28–43. PubMed ID: 21700266
- Traboulsi EI, Lenz W, Gonzales-Ramos M, Siegel J, Macrae WG, Maumenee IH. 1988. The Lenz microphthalmia syndrome. Am. J. Ophthalmol. 105: 40–45. PubMed ID: 3276203
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
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.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
- 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.
PGxome (Exome) Sequencing Panel
PGnome (Genome) Sequencing Panel
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2) Select Additional Test Options
STAT and Prenatal Test Options are not available with Patient Plus.
No Additional Test Options are available for this test.