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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.

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) 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

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

CFD

GPD1L

MAGT1

PRKCD

STAT3

ABCG5

CFH

HAX1

MALT1

PRKDC

STAT5B

ABCG8

CFHR1

HRAS

MAP2K1

PRKAG2

STIM1

ACTA2

CFHR3

ICOS

MAP2K2

PRKG1

STK4

ACTC1

CFHR5

IGHM

MEFV

PSMB8

TACI (TNFRSF13B)

ACTN2

CFI

IGLL1 (Lambda5)

MFAP5

PSTPIP1 (CD2BP1)

TAP1

ACVRL1 (ALK1)

CHD7

IKBKB

MPO

PTPN11

TAP2

ADA (ADA1)

CIITA

IKBKG (NEMO)

MS4A1 (CD20)

PTPRC (CD45)

TAPBP

ADA2 (CECR1)

COL5A1

IKZF1 (IKAROS)

MTHFD1

RAC2

TAZ

ADAMTS13

COL5A2

IL10

MVK

RAF1

TBX1

AICDA

CORO1A

IL10RA

MYBPC3

RAG1

TCAP

AK2

CR2 (CD21)

IL10RB

MYH11

RAG2

TCF3(E47)

AKAP9

CRYAB

IL1RN

MYH6

RASA1

TERC

ANK2

CSF2RA

IL21

MYH7

RASGRP2

TERT

ANKRD1

CSF3R

IL2R

MYL2

RBCK1 (HOIL1)

TGFB2

AP3B1 (HP2)

CSRP3

IL2RA (CD25)

MYL3

RBM8A

TGFB3

APOB

CTC1

IL2RG

MYLK

RBM20

TGFBR1

ATM

CTPS1

IL36RN

MYLK2

RFX5

TGFBR2

BLNK

CTSC

IL7R

MYOZ2

RFXANK

THBD

BRAF

CXCR4

ISG15

MYPN

RFXAP

TINF2

BTK

CYBA

ITCH

NCF2

RHOH

TMEM43

C3

CYBB

ITGB2

NCF4

RMRP

TNFRSF1A

CACNA1C

DCLRE1C (ARTEMIS)

ITK

NEXN

RNF168

TNFRSF13C

CACNA2D1

DES

JAK3

NFKB2

RTEL1

TNFRSF4 (OX40)

CACNB2

DGKE

JUP

NFKBIA (IKBA)

RYR2

TNFSF12 (TWEAK)

CARD11

DKC1

KCNE1

NHEJ1

SBDS

TNNC1

CARD14

DPYD

KCNE2

NHP2

SCN1B

TNNI3

CAV3

DSC2

KCNE3

NLRP12

SCN3B

TNNT2

CBL

DSG2

KCNH2

NLRP3 (C1AS1)

SCN4B

TPM1

CBS

DSP

KCNJ5

NOD2 (CARD15)

SCN5A

TRAC

CD19

DTNA

KCNJ8

NOP10

SEMA3E

TTC37

CD247 (CD3Z)

ELANE (ELA2)

KCNQ1

NOTCH1

SGCD

TTC7A

CD27

ENG

KRAS

NRAS

SH2D1A

TTN

CD3D

FBN1

LAMA4

ORAI1

SH3BP2

TTR

CD3E

FBN2

LAMP2

PCSK9

SHOC2

UNG

CD3G

FERMT3

LAMTOR2 (MAPBPIP)

PIK3R1

SKI

USB1 (C16ORF57)

CD40

FLNA

LCK

PIK3CD

SLC2A10

VCL

CD40LG

FOXN1

LDB3

PKLR

SLC37A4

VPS13B (COH1)

CD46 (MCP)

FOXP3

LDLR

PKP2

SLC46A1

VPS45

CD79A

FPR1

LDLRAP1

PLCG2

SMAD3

WAS

CD79B (B29)

G6PC3

LIG4

PLG

SMAD4

WIPF1

CD8A

GATA2

LMNA

PLN

SNTA1

WRAP53

CD81

GDF2 (BMP9)

LPIN2

PMM2 (CDG1)

SOS1

XIAP (BIRC4)

CEBPE

GFI1

LRBA

PNP

SPINK5

ZAP70

CFB

GLA

LRRC8A

 

 

 

  

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 36908-2
43567 Result Summary 50397-9
43568 Result Details 82939-0
43569 Interpretation In Process
43570 Additional Information 48767-8
43571 Method 49549-9
43572 Disclaimer 62364-5
43573 Reviewed by 18771-6

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

Forms

If not ordering electronically, complete, print, and send a Cardiovascular Test Request Form (T724) with the specimen.