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X-linked Lenz Microphthalmia Syndrome and Lethal Ogden Syndrome via the NAA10 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
NAA10 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8617NAA1081479 81479,81479 $990 Order Options and Pricing

Pricing Comments

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 platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks 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.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Dana Talsness, PhD

Clinical Features and Genetics

Clinical Features

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).

Testing Strategy

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.


Official Gene Symbol OMIM ID
NAA10 300013
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Lenz Microphthalmia Syndrome XL 309800
Ogden Syndrome XL 300855


  • 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


Ordering Options

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.

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.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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