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Cystic Fibrosis (139 common variants) – reflex to Poly T when CFS required 

Sample Reqs

A

Turnaround

5-7 days

Special instructions

Clinical history must be provided.

Test details

The table below shows the CFTR gene variants included in the Illumina TruSight Cystic Fibrosis 139-Variant Assay – listed by genomic coordinate order. These variants are expected to account for 95.4% of cystic fibrosis-causing alleles in a broad-spectrum population and identify approximately 91% of couples at risk through the detection of both disease-causing alleles.

Bold text indicates that these variants are part of the variant set recommended by the American College of Medical Genetics for cystic fibrosis screening published in 2023. Variants listed at the end of the table in italics are conditionally reported. For each variant the DNA nucleotide variant and the protein variant are given using HGVS nomenclature, followed by the legacy name.

c.1A>G p.(Met1Val)
M1V

c.1327_1330dup p.(Ile444Argfs*3)
1461ins4

c.2551C>T p.(Arg851*)
R851X

c.(53+1_54-1)_(273+1_274-1)del p.(?)
CFTRdele2,3

c.1364C>A p.(Ala455Glu)
A455E

c.2583del p.(Phe861Leufs*3)
2711delT

c.115C>T p.(Gln39*)
Q39X

C.1393-1G>A p.(?)
1525-1G>A

c.2657+5G>A p.(?)
2789+5G>A

c.178G>T p.(Glu60*)
E60X

c.1397C>A p.(Ser466*)
S466X (C>A)

c.2668C>T p.(Gln890*)
Q890X

c.200C>T p.(Pro67Leu)
P67L

c.1397C>G p.(Ser466*)
S466X (C>G)

c.2780T>C p.(Leu927Pro)
L927P

c.223C>T p.(Arg75*)
R75X

c.1400T>C p.(Leu467Pro)
L467P

c.2834C>T p.(Ser945Leu)
S945L

c.254G>A p.(Gly85Glu)
G85E

c.1418del p.(Gly473Glufs*54)
1548delG

c.2875del p.(Ala959Hisfs*9)
3007delG

c.262_263del p.(Leu88Ilefs*22)
394delTT

c.1466C>A p.(Ser489*)
S489X

c.2908G>C p.(Gly970Arg)
G970R

c.273+1G>A p.(?)
405+1G>A

c.1475C>T p.(Ser492Phe)
S492F

c.2988G>A p.(Gln996=)
3120G>A

c.274-1G>A p.(?)
406-1G>A

c.1477C>T p.(Gln493*)
Q493X

c.2988+1G>A p.(?)
3120+1G>A

c.274G>T p.(Glu92*)
E92X

c.1519_1521del p.(Ile507del)
I507del

c.2989-1G>A p.(?)
3121-1G>A

c.274G>A p.(Glu92Lys)
E92K

c.1521_1523del p.(Phe508del)
F508del

c.3140-26A>G p.(?)
3272-26A>G

c.292C>T p.(Gln98*)
Q98X

c.1545_1546del p.(Tyr515*)
1677delTA

c.3194T>C p.(Leu1065Pro)
L1065P

c.325_327delinsG p.(Tyr109Glyfs*4)
457TAT>G

c.1558G>T p.(Val520Phe)
V520F

c.3196C>T p.(Arg1066Cys)
R1066C

c.328G>C p.(Asp110His)
D110H

c.1573C>T p.(Gln525*)
Q525X

c.3197G>A p.(Arg1066His)
R1066H

c.349C>T p.(Arg117Cys)
R117C

c.1585-8G>A p.(?)
1717-8G>A

c.3230T>C p.(Leu1077Pro)
L1077P

c.350G>A p.(Arg117His)
R117H

c.1585-1G>A p.(?)
1717-1G>A

c.3266G>A p.(Trp1089*)
W1089X

c.366T>A p.(Tyr122*)
Y122X

c.1624G>T p.(Gly542*)
G542X

c.3276C>A p.(Tyr1092*)
Y1092X (C>A)

c.442del p.(Ile148Leufs*5)
574delA

c.1645A>C p.(Ser549Arg)
S549R

C.3276C>G p.(Tyr1092*)
Y1092X (C>G)

c.489+1G>T p.(?)
621+1G>T

c.1646G>A p.(Ser549Asn)
S549N

c.3302T>A p.(Met1101Lys)
M1101K

c.531del p.(Ile177Metfs*12)
663delT

c.1647T>G p.(Ser549Arg)
S549R

c.3310G>T p.(Glu1104*)
E1104X

c.532G>A p.(Gly178Arg)
G178R

c.1652G>A p.(Gly551Asp)
G551D

c.3472C>T p.(Arg1158*)
R1158X

c.579+1G>T p.(?)
711+1G>T

c.1654C>T p.(Gln552*)
Q552X

c.3484C>T p.(Arg1162*)
R1162X

c.579+3A>G p.(?)
711+3A>G

c.1657C>T p.(Arg553*)
R553X

c.3528del p.(Lys1177Serfs*15)
3659delC

c.579+5G>A p.(?)
711+5G>A

c.1675G>A p.(Ala559Thr)
A559T

c.3587C>G p.(Ser1196*)
S1196X

c.580-1G>T p.(?)
712-1G>T

c.1679G>C p.(Arg560Thr)
R560T

c.3611G>A p.(Trp1204*)
W1204X

c.595C>T p.(His199Tyr)
H199Y

c.1679G>A p.(Arg560Lys)
R560K

c.3612G>A p.(Trp1204*)
W1204X

c.613C>T p.(Pro205Ser)
P205S

c.1680-886A>G p.(?)
1811+1634A>G

c.3659del p.(Thr1220Lysfs*8)
3791delC

c.617T>G p.(Leu206Trp)
L206W

c.1680-1G>A p.(?)
1812-1G>A

c.3718-2477C>T p.(?)
3849+10kbC>T

c.658C>T p.(Gln220*)
Q220X

c.1753G>T p.(Glu585*)
E585X

c.3731G>A p.(Gly1244Glu)
G1244E

c.723_743+1del p.(?)
852del22

c.1766+1G>A p.(?)
1898+1G>A

c.3744del p.(Lys1250Argfs*9)
3876delA

c.948del p.(Phe316Leufs*12)
1078delT

c.1766+3A>G p.(?)
1898+3A>G

c.3752G>A p.(Ser1251Asn)
S1251N

c.988G>T p.(p.Gly330*)
G330X

c.2012del p.(Leu671*)
2143delT

c.3773dup p.(Leu1258Phefs*7)
3905insT

c.1000C>T p.(Arg334Trp)
R334W

c.2051_2052delinsG p.(Lys684Serfs*38)
2183AA>G

c.3846G>A p.(Trp1282*)
W1282X

c.1007T>A p.(Ile336Lys)
I336K

c.2052del p.(Lys684Asnfs*38)
2184delA

c.3873+1G>A p.(?)
4005+1G>A

c.1013C>T p.(Thr338Ile)
T338I

c.2052dup p.(Gln685Thrfs*4)
2184insA

c.3889dup p.(Ser1297Phefs*5)
4016insT

c.1021T>C p.(Ser341Pro)
S341P

c.2125C>T p.(Arg709*)
R709X

c.3909C>G p.(Asn1303Lys)
N1303K

c.1021_1022dup p.(Phe342Hisfs*28)
1154insTC

c.2128A>T p.(Lys710*)
K710X

c.3937C>T p.(Gln1313*)
Q1313X

c.1040G>A p.(Arg347His)
R347H

c.2175dup p.(Glu726Argfs*4)
2307insA

c.4077_4080delinsAA p.(Val1360Thrfs*3)
4209TGTT>AA

c.1040G>C p.(Arg347Pro)
R347P

c.2195T>G p.(Leu732*)
L732X

c.(3963+1_3964-1)_(4242+1_4243-1)del p.(?)
CFTRdele22,23

c.1055G>A p(Arg352Gln)
R352Q

c.2215del p.(Val739Tyrfs*16)
2347delG

c.4251del p.(Glu1418Argfs*14)
4382delA

c.1081del p.(Trp361Glyfs*8)
1213delT

c.2290C>T p.(Arg764*)
R764X

 

c.1116+1G>A p.(?)
1248+1G>A

c.2453del p.(Leu818Trpfs*3)
2585delT

 

c.1130dup p.(Gln378Alafs*4)
1259insA

c.2464G>T p.(Glu822*)
E822X

PolyTG/PolyT tract

c.1202G>A p.(Trp401*)
W401X

c.2490+1G>A p.(?)
2622+1G>A

c.1516A>G p.(Ile506Val)
I506V

c.1203G>A p.(Trp401*)
W401X

c.2491G>T p.(Glu831*)
E831X

c.1519A>G p.(Ile507Val)
I507V

c.1209+1G>A p.(?)
1341+1G>A

c.2537G>A p.(Trp846*)
W846X

c.1523T>G p.(Phe508Cys)
F508C

Further information about the clinical relevance/impact of these variants can be found at www.cftr2.org

Further information about the variants recommended by the ACMG can be found at https://doi.org/10.1016/j.gim.2023.100867

Further information about the nomenclature used for variant naming can be found at www.hgvs.org



Sample type guide

A

Lavender Vacutainer, EDTA anticoagulant, 4ml/10ml(10ml EDTA tubes are used for specific PCR assays)

Additional information

Last-updated: 14/03/23

 

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