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Lynch Syndrome via the MSH2 Exons 1-7 Inversion

Summary and Pricing

Test Method

Targeted Deletion Testing via PCR
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
MSH2 81479 81479 $350
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
906MSH281479 81479 $350 Order Options and Pricing

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Turnaround Time

4 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.


Genetic Counselors


  • Yuan Xue, PhD

Clinical Features and Genetics

Clinical Features

Lynch Syndrome, also called Hereditary Nonpolyposis Colorectal Cancer (HNPCC), is an inherited cancer syndrome caused by germline pathogenic variants in DNA mismatch repair (MMR) genes. MMR genes encode proteins that repair small sequence errors, or mismatches, during DNA replication. Pathogenic variants in a single mismatch repair gene can cause widespread genomic instability characterized by the expansion or contraction of short tandem repeat sequences, or microsatellites (Grady and Carethers. 2008. PubMed ID: 18773902). This phenomenon of microsatellite instability (MSI) leads to somatic mutations in oncogenes and/or tumor suppressor genes, including TGFβIIR and NF1 among others (Wang et al. 2003. PubMed ID: 12522551). As a result, Lynch Syndrome is marked by early onset and high lifetime risk of cancer, particularly in the right colon but also in the endometrium, ovary, stomach, bile duct, kidney, bladder, ureter, and brain (Jang and Chung. 2010. PubMed ID: 20559516). Clinical hallmarks of Lynch Syndrome, as delineated by the Amsterdam criteria, include heritable colorectal (Type I) or extracolonic (Type II) cancer, present in at least three relatives over at least two consecutive generations, with an onset of cancer before the age of 50 in at least one case, and pathological MSI within tumors (Vasen et al. 1999. PubMed ID: 10348829).


Lynch syndrome is an autosomal dominant disease caused by germline variants in one of five described MMR genes: MLH1, MSH2, MSH6, PMS2 and EPCAM (Idos and Valle. 2021. PubMed ID: 20301390).

A germline inversion of exons 1-7 in MSH2 has been reported in fourteen individuals from eleven unrelated families clinically presenting with Lynch syndrome associated phenotypes including colorectal, endometrial, gastric, and ovarian cancer (Wagner et al. 2002. PubMed ID: 12203789; Rhees et al. 2013. PubMed ID: 24114314; Mork et al. 2016. PubMed ID: 28004223).

Clinical Sensitivity - Targeted Deletion

The clinical sensitivity of the MSH2 inversion is not currently known, but this inversion appears to be a relatively rare cause of Lynch Syndrome.

Testing Strategy

This assay tests for the inversion of exons 1-7 in MSH2 using a PCR based method using primers and approach described in Rhees et al. 2013. PubMed ID: 24114314.

Indications for Test

Candidates for this test are patients with a Lynch Syndrome diagnosis who may have tested negative for Lynch syndrome using standard methodologies (NGS/aCGH), and relatives of patients who have a verified MSH2 inversion. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.


Official Gene Symbol OMIM ID
MSH2 609309
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Lynch Syndrome I AD 120435

Related Tests

Colorectal Cancer Predisposition via the POLD1 Gene
Colorectal Cancer Predisposition via the POLE Gene
Hereditary Breast and Ovarian Cancer - High Risk and Lynch Syndrome Panel
Hereditary Endometrial Cancer Panel
Lynch Syndrome Panel
Lynch Syndrome via the EPCAM Gene
Lynch Syndrome via the MLH1 Gene
Lynch Syndrome via the MLH3 Gene
Lynch Syndrome via the MSH2 Gene
Lynch Syndrome via the PMS2 Gene
Lynch Syndrome via MSH6 Gene



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

Specimen Types

Specimen Requirements and Shipping Details

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