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Test Code KVAR1 Known Variant Analysis-1 Variant

Secondary ID

65065

Useful For

Diagnostic or predictive testing for specific conditions when a DNA sequence variant of interest has been previously identified in a family member, and follow-up testing for this specific variant in other family members is desired

 

Carrier screening for individuals at risk for having a DNA sequence variant that was previously identified in a family member

 

Segregation analysis for a single familial DNA sequence variant

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 variant was 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 (KVAR1) 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-1 Variant

Specimen Type

Varies


Advisory Information


This test can only be performed if a variant has previously been identified in a family member of this individual.

 

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



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.



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 variant 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

Reject Due To

Hemolysis

NA

Lipemia

NA

Icterus

NA

Other

NA

Clinical Information

This test is available for analysis of the presence of 1 sequence variant (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 http://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.

 

Testing may be delayed if required documentation (ie, patient information sheet) is not received.

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

Performing Laboratory

Mayo Medical Laboratories in Rochester

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

LOINC Code Information

Test ID Test Order Name Order LOINC Value
KVAR1 Known Variant Analysis-1 Variant In Process

 

Result ID Test Result Name Result LOINC Value
43923 Variant Tested 82939-0
43544 Result Summary 50397-9
43545 Result Details In Process
43546 Interpretation In Process
43547 Additional Information 48767-8
43548 Method 49549-9
43549 Disclaimer 62364-5
43550 Reviewed by In Process

Forms

1. Known Variant Analysis: Required Patient Information (T768) is required, see Special Instructions.

2. New York Clients-Informed consent is required. Please document on the request form or electronic order that a copy is on file. An Informed Consent for Genetic Testing (T576) is available in Special Instructions.

3. If not ordering electronically, complete, print, and send a Cardiovascular Test Request Form (T724) with the specimen (http://www.mayomedicallaboratories.com/it-mmfiles/cardiovascular-request-form.pdf).

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
MATCC Maternal Cell Contamination, B Yes No
CULFB Fibroblast Culture for Genetic Test Yes No
CULAF Amniotic Fluid Culture/Genetic Test Yes No

Disease States

  • Common variable immunodeficiency