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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.



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) 4 days/Refrigerated 14 days

 

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

CFH

HAX1

MALT1

PRKDC

STAT5B

ACTA2

CFHR1

HRAS

MAP2K1

PRKAG2

STIM1

ACTC1

CFHR3

ICOS

MAP2K2

PRKG1

STK4

ACTN2

CFHR5

IGHM

MEFV

PSMB8

TACI (TNFRSF13B)

ACVRL1

CFI

IGLL1 (Lambda5)

MFAP5

PSTPIP1 (CD2BP1)

TAP1

ADA (ADA1)

CHD7

IKBKB

MPO

PTPN11

TAP2

ADA2 (CECR1)

CIITA

IKBKG (NEMO)

MS4A1 (CD20)

PTPRC (CD45)

TAPBP

ADAMTS13

COL5A1

IKZF1 (IKAROS)

MTHFD1

RAC2

TAZ

AICDA

COL5A2

IL10

MVK

RAF1

TBX1

AK2

CORO1A

IL10RA

MYBPC3

RAG1

TCAP

AKAP9

CR2 (CD21)

IL10RB

MYH11

RAG2

TCF3(E47)

ANK2

CRYAB

IL1RN

MYH6

RASGRP2

TERC

ANKRD1

CSF2RA

IL21

MYH7

RBCK1 (HOIL1)

TERT

AP3B1 (HP2)

CSF3R

IL2R

MYL2

RBM8A

TGFB2

APOB

CSRP3

IL2RA (CD25)

MYL3

RBM20

TGFB3

ATM

CTC1

IL2RG

MYLK

RFX5

TGFBR1

BLNK

CTPS1

IL36RN

MYLK2

RFXANK

TGFBR2

BRAF

CTSC

IL7R

MYOZ2

RFXAP

THBD

BTK

CXCR4

ISG15

MYPN

RHOH

TINF2

C3

CYBA

ITCH

NCF2

RMRP

TMEM43

CACNA1C

CYBB

ITGB2

NCF4

RNF168

TNFRSF1A

CACNA2D1

DCLRE1C (ARTEMIS)

ITK

NEXN

RTEL1

TNFRSF13C

CACNB2

DES

JAK3

NFKB2

RYR2

TNFRSF4 (OX40)

CARD11

DGKE

JUP

NFKBIA (IKBA)

SBDS

TNFSF12 (TWEAK)

CARD14

DKC1

KCNE1

NHEJ1

SCN1B

TNNC1

CAV3

DPYD

KCNE2

NHP2

SCN3B

TNNI3

CBL

DSC2

KCNE3

NLRP12

SCN4B

TNNT2

CBS

DSG2

KCNH2

NLRP3 (C1AS1)

SCN5A

TPM1

CD19

DSP

KCNJ5

NOD2 (CARD15)

SEMA3E

TRAC

CD247 (CD3Z)

DTNA

KCNJ8

NOP10

SGCD

TTC37

CD27

ELANE (ELA2)

KCNQ1

NOTCH1

SH2D1A

TTC7A

CD3D

ENG

KRAS

NRAS

SH3BP2

TTN

CD3E

FBN1

LAMA4

ORAI1

SHOC2

TTR

CD3G

FBN2

LAMP2

PIK3R1

SKI

UNG

CD40

FERMT3

LAMTOR2 (MAPBPIP)

PIK3CD

SLC2A10

USB1 (C16ORF57)

CD40LG

FLNA

LCK

PKLR

SLC37A4

VCL

CD46 (MCP)

FOXN1

LDB3

PKP2

SLC46A1

VPS13B (COH1)

CD79A

FOXP3

LDLR

PLCG2

SMAD3

VPS45

CD79B (B29)

FPR1

LIG4

PLG

SMAD4

WAS

CD8A

G6PC3

LMNA

PLN

SNTA1

WIPF1

CD81

GATA2

LPIN2

PMM2 (CDG1)

SOS1

WRAP53

CEBPE

GFI1

LRBA

PNP

SPINK5

XIAP (BIRC4)

CFB

GLA

LRRC8A

PRKCD

STAT3

ZAP70

CFD

GPD1L

MAGT1

 

 

 

 

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.

 

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 82939-0
43546 Interpretation In Process
43547 Additional Information 48767-8
43548 Method 49549-9
43549 Disclaimer 62364-5
43550 Reviewed by 18771-6

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