Ordering Recommendation

Detect germline MSH6 variants. Use in MMR-deficient carcinoma with suggestive IHC results (isolated loss of MSH6 protein).


Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification




28-35 days

New York DOH Approval Status
This test is New York DOH approved.
Specimen Required
Patient Preparation

Lavender (K2EDTA), Pink (K2EDTA), or Yellow (ACD Solution A or B).

Specimen Preparation

Transport 3 mL whole blood. (Min: 1 mL)

Storage/Transport Temperature


Unacceptable Conditions

Ambient: 1 week; Refrigerated: 1 month; Frozen: 6 months

Reference Interval
Interpretive Data

Background Information for HNPCC/Lynch Syndrome (MSH6) Sequencing and Deletion/Duplication:
Increased risk of colorectal and extra-colonic cancers including endometrial, renal pelvis, ureter, ovary, stomach, small intestine, and hepatobiliary tract.
1-2 percent of colorectal cancer is due to mismatch repair gene mutations.
Autosomal dominant
Penetranceof MSH6 Mutations:
Risk of colorectal cancer is 40 percent in men and 20 percent in women up to age 80. Women also have a 40 percent risk for endometrial cancer up to age 80.
Pathogenic germline MLH1, MSH2, MSH6, and PMS2 gene mutations.
Gene Tested:
Clinical Sensitivity: Approximately 5 percent of Lynch syndrome is due to MSH6 mutations.
Bidirectional sequencing of MSH6 coding regions and intron-exon boundaries; multiplex ligation-dependent probe amplification (MLPA) to detect large MSH6 exonic deletions.
Test Limitations:
Diagnostic errors can occur due to rare sequence variations. The breakpoints of large deletions/duplications will not be determined. Regulatory region, deep intronic mutations and mutations in genes other than MSH6 will not be detected. This assay is not designed to detect somatic variants associated with malignancy. Interpretation of this test result may be impacted if the patient has had an allogeneic stem cell transplantation.

Compliance Statement C: For human genetic inheritable conditions and mutations. This test was developed and its performance characteristics determined by ARUP Laboratories. The U. S. Food and Drug Administration has not approved or cleared this test; however, FDA clearance or approval is not currently required for clinical use. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions.

Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Hotline History
CPT Codes

81298; 81300

Component Test Code* Component Chart Name LOINC
0051657 Lynch Syndrome (MSH6) Interpretation 35379-7
2001368 MSH6 FGA Specimen 31208-2
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.
  • hMSH6 genotyping
  • HMSH6 germline assay
  • MSH6 Full Gene Analysis
  • MSH6 gene testing
HNPCC/Lynch Syndrome (MSH6) Sequencing and Deletion/Duplication