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Test ID: KVAR3 Known Variant Analysis-3+ Variants

Useful For

Diagnostic or predictive testing for specific conditions when 3 to 5 DNA sequence variants of interest have been previously identified in a family member, and follow-up testing for these specific variants in other family members is desired

 

Carrier screening for individuals at risk for having 3 to 5 DNA sequence variants that were previously identified in a family member

 

Segregation analysis for 3 to 5 familial DNA sequence variants

Testing Algorithm

For prenatal specimens only: If amniotic fluid (nonconfluent cultured cells) is received, amniotic fluid culture will be added and charged separately. If chorionic villus specimen (nonconfluent cultured cells) is received, fibroblast culture will be added and charged separately. For any prenatal specimen that is received, maternal cell contamination studies will be added.

 

If the familial variants were previously identified at an outside laboratory, sending DNA from a family member with a positive genetic test result to be used as a positive control is strongly recommended to ensure that the specific familial variant can be detected by our laboratory. Proband samples should be sent as a separate (KVAR3) order, under the proband's identifiers (ie, do not send the patient and proband samples under the same order). If a positive control is not provided, negative results will be reported with a stated limitation that the laboratory's ability to detect the familial variant has not been confirmed and a false-negative result cannot be ruled out.

 

See Familial/Autosomal Dominant Hypercholesterolemia Diagnostic Algorithm in Special Instructions.

Method Name

Polymerase Chain Reaction (PCR) Followed by DNA Sequencing Analysis

Reporting Name

Known Variant Analysis-3+ Variants

Specimen Type

Varies


Advisory Information


This test can only be performed if 3 to 5 variants have previously been identified in a family member of this individual. If only 2 variants have been identified, order KVAR2 / Known Variant Analysis-2 Variant. If only 1 variant has been identified, order KVAR1 /Known Variant Analysis-1 Variant.



Additional Testing Requirements


All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis on the maternal specimen.

 

If the 3 to 5 familial variants were previously identified at an outside laboratory, sending DNA from a family member with a positive genetic test result to be used as a positive control is strongly recommended to ensure that the specific familial variant can be detected by our laboratory. Proband samples should be sent as a separate (KVAR3) order, under the proband's identifiers (ie, do not send the patient and proband samples under the same order).



Shipping Instructions


Prenatal specimens can be sent Monday through Thursday and must be received by 5 p.m. CST on Friday in order to be processed appropriately.



Necessary Information


Known Variant Analysis: Required Patient Information form (T768) with documentation of the specific familial variants is required. See Special Instructions. Testing will be held until information is received. If information is not received within 14 days of sample receipt, testing may be canceled.



Specimen Required


Submit only 1 of the following specimen types:

 

Specimen Type: Whole blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 3 mL

Collection Instructions: Send specimen in original tube.

Specimen Stability Information: Ambient (preferred)/Refrigerated

 

Specimen Type: DNA

Container/Tube: 2 mL screw top tube

Specimen Volume: 100 mcL (microliters)

Collection Instructions:

1. The preferred volume is 100 mcL at a concentration of 250 ng/mcL.

2. Include concentration and volume on tube.

Specimen Stability Information: Frozen (preferred)/Ambient/Refrigerated 

 

Prenatal Specimens

Due to the complexity of prenatal testing, consultation with the laboratory is required for all prenatal testing.

 

Specimen Type: Amniotic fluid

Container/Tube: Amniotic fluid container

Specimen Volume: 20 mL

Specimen Stability Information: Refrigerated (preferred)/Ambient

Additional Information: A separate culture charge will be assessed under CULAF / Amniotic Fluid Culture for Genetic Testing.

 

Specimen Type: Cultured amniocytes

Container/Tube: T-25 flask

Specimen Volume: 2 Full flasks

Collection Instructions: Submit confluent cultured cells from another laboratory.

Specimen Stability Information: Ambient (preferred)/Refrigerated

 

Specimen Type: Chorionic villi

Container/Tube: 15-mL tube containing 15-mL of transport media

Specimen Volume: 20 mg

Specimen Stability Information: Refrigerated

Additional Information: A separate culture charge will be assessed under CULFB / Fibroblast Culture for Genetic Testing.

 

Specimen Type: Cultured chorionic villi

Container/Tube: T-25 flasks

Specimen Volume: 2 Full flasks

Collection Instructions: Submit confluent cultured cells from another laboratory.

Specimen Stability Information: Ambient (preferred)/Refrigerated


Specimen Minimum Volume

Whole Blood: 0.6 mL; Amniotic Fluid: 10 mL; Chorionic Villi: 5 mg

Specimen Stability Information

Specimen Type Temperature Time
Varies Varies

Clinical Information

This test is for analysis of the presence of 3 to 5 sequence variants (nucleotide substitution or small insertion or deletion of nucleotides) previously identified in a family member. Targeted testing is used for diagnostic or predictive testing in cases in which variants have been previously identified in an affected family member. This testing is also used for segregation analysis to determine whether a particular variant or variants are segregating with the phenotype in an affected family. This test is used for a specific subset of genes only.

 

 

Genes Available for Testing 

ABCC9

DTNA

MYBPC3

SCN5A

ACTA2

ENG

MYH11

SGCD

ACTC1

FBN1

MYH6

SHOC2

ACTN2

FBN2

MYH7

SKI

ACVRL1

GLA

MYL2

SLC2A10

AKAP9

GPD1L

MYL3

SMAD3

ANK2

HRAS

MYLK

SNTA1

ANKRD1

JUP

MYLK2

SOS1

APOB

KCNE1

MYOZ2

TACI (TNFRSF13B)

BRAF

KCNE2

MYPN

TAZ

CACNA1C

KCNE3

NEXN

TCAP

CACNA2D1

KCNH2

NRAS

TGFB2

CACNB2

KCNJ5

PKLR

TGFBR1

CAV3

KCNJ8

PKP2

TGFBR2

CBL

KCNQ1

PLN

TMEM43

CBS

KRAS

PRKAG2

TNNC1

COL3A1

LAMA4

PTPN11

TNNI3

CRYAB

LAMP2

RAF1

TNNT2

CSRP3

LDB3

RBM20

TPM1

DES

LDLR

RYR2

TTN

DSC2

LMNA

SCN1B

TTR

DSG2

MAP2K1

SCN3B

VCL

DSP

MAP2K2

SCN4B

 

 

Refer to the following resources for information regarding the listed gene targets. GeneReviews-NCBI Bookshelf, available at www.ncbi.nlm.nih.gov/books/NBK1116/ or OMIM, available at www.omim.org/.

 

If testing is needed for a gene not on this list, see FMTT / Familial Mutation, Targeted Testing, which includes targeted/site-specific testing for additional genes.

Reference Values

An interpretive report will be provided.

Interpretation

Evaluation and categorization of variants is performed using the most recent published American College of Medical Genetics and Genomics recommendations as a guideline.(1) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Clinical Reference

1. Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015;17(5):405-424

Day(s) and Time(s) Performed

Varies

Analytic Time

10 days

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

81403 x 3 (up to x 5)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
KVAR3 Known Variant Analysis-3+ Variants In Process

 

Result ID Test Result Name Result LOINC Value
48265 Variant Tested In Process
43567 Result Summary 50397-9
43568 Result Details In Process
43569 Interpretation In Process
43570 Additional Information 48767-8
43571 Method 49549-9
43572 Disclaimer 62364-5
43573 Reviewed by In Process