Elexacaftor-tezacaftor-ivacaftor in people with cystic fibrosis harbouring two CFTR Class I variants: real-world data from the French compassionate programme

Summary

Background

The European Medicines Agency has recently expanded the label of elexacaftor-tezacaftor-ivacaftor (ETI) to all people with cystic fibrosis (pwCF) aged 2 years and older who have at least one non-Class I mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. No large-scale data exist on the use of ETI in pwCF harbouring two Class I CFTR variants.

Methods

PwCF with two Class I variants who received ETI for an individual 4–6 week trial were identified within the real-world French compassionate programme and their response to ETI, as assessed by a centralized adjudication committee, was evaluated based on evolution of clinical data, lung function and sweat chloride. The lists of Class I CFTR variants were established using data from the CFTR2 and CFTR-France databases.

Findings

Among 652 participants who were recruited in the French compassionate programme from May 19, 2022, to March 26, 2025, 163 had two Class I variants and received ETI. 155 (95%) were considered as non-responders and stopped ETI, whereas 8 (5%) were considered as responders and continued ETI. The six Class I variants probably responsive to ETI were: E831X and 4374+1G > A (each present in 2 participants), 1716+2T > C, 4382delA, 875+1G > A and CFTRdup1-3 (each present in 1 participant). Using CFTR2 and CFTR-France databases, a list of 955 true (i.e., shown or presumed to lead to the absence of CFTR protein) Class I variants was established. True Class I variants are predicted to be non-responsive to ETI and clinical evidence of the lack of response to ETI was confirmed in the French compassionate programme for 108 variants within this list. A second list of 78 exceptional (i.e., in which a CFTR protein may be produced) Class I variants was further established: clinical data on ETI responsiveness was available for 11 exceptional Class I variants of which six were found probably responsive and five probably non-responsive to ETI.

Interpretation

Class I variants are usually not responsive to ETI and pwCF with two true Class I variants should not be treated with ETI. However, exceptional Class I CFTR variants may lead to protein production, providing a substrate for ETI. In pwCF harbouring at least one of these exceptional Class I variants, an individual trial of ETI should be granted.

Funding

Association Vaincre la Mucoviscidose, Société Française de la Mucoviscidose, Filière Maladies Rares MUCO-CFTR.

Research in context.

Evidence before this study

A search was conducted in PubMed on August 8, 2025 with no time limit, to identify articles on the effect of elexacaftor-tezacaftor-ivacaftor (ETI) treatment in people with cystic fibrosis (pwCF) carrying two Class I cystic fibrosis transmembrane conductance regulator (CFTR) variants. Search terms were “elexacaftor” and “Class I CFTR”; 33 articles were identified, none of which contained clinical data on ETI's effect on in humans. Because the effect of ETI depends on enhancing existing production and functionality of the CFTR protein, responses to ETI may occur only in people harboring variants for which some CFTR protein is produced. We hypothesized that Class I variants are heterogeneous with some variants resulting in CFTR protein production and response to ETI.

Added value of this study

This study describes a large cohort of people with CF with two Class I variants who received an individual trial of ETI for 4–6 weeks, as part of the French compassionate programme. Among 163 participants with two Class I variants who received ETI, 95% were considered non-responders, whereas 5% were responders by a centralized adjudication committee. The responders harboured at least one Class I variant with particular characteristics leading to CFTR protein synthesis and which made them exceptions to the group of variants typically considered Class I. We then used the CFTR2 and CFTR-France databases to establish lists of true (predicted or shown to produce no CFTR protein) and exceptional (predicted or shown to produce a CFTR protein) Class I variants. Among 955 true Class I variants, 108 variants were present in participants who received ETI in the French compassionate programme; all were non-responsive. Among 78 Class I variants defined as exceptional, 6 were responsive and 5 were non-responsive in the French compassionate programme, the remaining variants being not present in this programme.

Implications of all the available evidence

The initial labels for ETI were limited to F508del and were based on results from clinical trials. In December 2020, the United State Food and Drug Administration (FDA) expanded the label to include 177 variants for which in vitro data suggested a positive response to ETI; the FDA subsequently used the same approach to further expand the list of eligible variants to an additional 94 variants in December 2024. Real-world programmes, in which participants received ETI, showed that many variants not approved by the FDA were responsive to ETI, whereas other variants, including nonsense variants, were non-responsive. The label expansion released by the EMA in April 2025 allowed expanded access to ETI for most pwCF, excluding only those with two Class I variants. Our data indicate that the vast majority of Class I variants are non-responsive to ETI, but that exceptional Class I variants may be responsive. Additionally, several non-Class I variants (e.g., I507del [c.1519_1521del]), a prevalent Class II variant) are also non-responsive to ETI. The EMA label is a major step forward as it allows most people with CF to become eligible for ETI; however, selected genotypes within the label may be non-responsive to ETI, whereas others not included in the label may be responsive. For treating clinicians, it appears that establishing lists of responsive and non-responsive variants to ETI is an important goal.

Introduction

Elexacaftor-tezacaftor-ivacaftor (ETI) is a combination of CFTR modulators initially developed for people with cystic fibrosis (pwCF) harbouring at least one F508del (c.1521_1523del) variant1, 2, 3 and approved in this indication in multiple countries. Fiedorczuk et al. reported that individual components of ETI bind to the misfolded CFTR protein, improving its 3D conformation and partially restoring ion transport.⁴ Thus, the presence of CFTR protein substrate appears critical to the action of ETI and the absence of CFTR protein is predicted to result in the lack of effect of ETI.

Over the past five years, ETI has further proven effective in selected non-F508del, often rare, CFTR variants. In December 2020, the US Food and Drug Administration (FDA) approved ETI for pwCF with at least one of 177 non-F508del rare CFTR variants based on in vitro data produced in Fisher Rat Thyroid (FRT) cells stably transfected with CFTR variants.⁵ Cromwell et al. recently published data from the US Cystic Fibrosis Foundation (CFF) registry, showing improved percent predicted forced expiratory volume in 1 s (ppFEV₁) and reduced rates of pulmonary exacerbations in pwCF with no F508del, but harbouring at least one of the 177 FDA-approved variants, confirming the predictive value of positive response in FRT cells.⁶ In December 2024, the FDA further approved the use of ETI in 94 additional rare variants based on FRT cell data. Real-world use of ETI has further shown that many CFTR variants, including both FDA-approved and non-FDA approved variants, are responsive to ETI.^7,8 In April 2025, taking into account results from FRT cells, clinical trials, and real-world studies, the European Medicines Agency (EMA) approved ETI in pwCF “aged 2 years and older, who have at least one non-Class I mutation in the CFTR gene”. This label implies that pwCF harbouring two Class I variants are not eligible to ETI in Europe; but importantly, no list of Class I variants was provided, leaving the prescribing clinicians in need for clarification.

Soon after the discovery of the CFTR gene in 1989, Welsh and Smith proposed a four-class classification of the relationship between CFTR variants and defect in CFTR function,⁹ which was then supplemented by two additional functional classes.^10,11 Class I of CFTR variants was defined by defective protein synthesis, thus providing no protein target to CFTR modulators. Overall, variants typically falling in this class are nonsense, canonical splice site variants, small insertions or deletions that result in a premature termination codon (frameshift), exon deletions or duplications, and start-loss variants (variants that impair the translation initiation). However, not all variants belonging to one of these categories meet the criterion of “absence of functional CFTR at the epithelial cell surface” and no comprehensive list of Class I variants is currently available. In fact, some variants appearing to be Class I may result in the production of a normal residual or abnormal protein, potentially rescuable by CFTR modulators. Historically, the class system has been useful in defining broad groupings of CFTR variants, but it now lacks nuance as knowledge regarding variant mechanisms has increased. A single variant may have characteristics of multiple classes^12,13 but is often defined by its predominant or first-discovered defect, and some classes are defined by defects that result from slightly different pathways.¹⁴ Assignment of class does not always adequately describe a variant's functional effect, which may impact multiple steps during transcription and translation, and may be difficult to use in determining responsiveness to therapy.

In the present study, we hypothesized that within the group of Class I variants, some may be responsive to ETI. We thus reviewed the data contained in the ongoing French compassionate programme,^7,8 in which pwCF with no F508del variant were granted a 4–6 weeks trial of ETI, whose effectiveness or non-effectiveness was determined using all available information by a centralized adjudication committee at the end of this initial treatment period. The purpose of this analysis was (A) to examine the response to ETI in participants with two Class I variants (B) to establish lists of Class I variants, for helping the prescribing clinicians to determine which pwCF are not eligible and which people may be eligible for ETI in Europe.

Methods

The French compassionate programme

The French compassionate programme has been described in detail in previous reports.^7,8 Briefly, eligible pwCF were aged 6 years and older, had no F508del variant, and no previous lung transplantation. Participants were granted a 4–6 weeks trial of ETI, prescribed at doses recommended by the manufacturer. At the end of this initial treatment period, effectiveness was judged by a centralized adjudication committee, which analyzed all available data including clinical data, other treatments (e.g., the use of antibiotics for a pulmonary exacerbation), sweat chloride concentration (SCC), and percent predicted forced expiratory volume in 1 s (ppFEV₁) prior to and after ETI initiation; chest CT imaging was also examined when available. PwCF that were identified as responders were able to continue treatment thereafter, and non-responders stopped ETI after the 4–6 week trial.^7,8

Ethics

All patients received written information about the aims and design of the study and were informed about the use of their personal medical data for research purposes. Written informed consent was not required under French law. The study was approved by the institutional review board of the French Society for Respiratory Medicine (#2020–003). For the present analyses, all available data as per March 26, 2025 were analysed, including previously published^7,8 and unpublished cases.

Definition of CFTR Class I variants and establishing the lists of true and exceptional Class I CFTR variants

Class I of CFTR variants was historically defined by defective protein synthesis, with absence of functional CFTR at the epithelial cell surface.^9,15, 16, 17 First, we have compiled a global list of all variants expected to lead to complete absence of CFTR protein reported in the CFTR2 (available at https://cftr2.org/)¹⁸ and the CFTR-France (available at https://cftr.chu-montpellier.fr/) databases.¹⁹ Variants included in this list were: nonsense variants (i.e., point variations predicted to result in a premature stop codon), variants that impact canonical splice sites (i.e., variants in the +1, +2 or −1, −2 positions of intronic sequences), small insertions or deletions (i.e., frameshifts predicted to result in a premature termination codon), start-loss variants (i.e., resulting in the loss of the first ATG), and large exon deletions or duplications.

We defined true Class I variants as variants that result in no protein synthesis or are predicted to result in no protein synthesis, whereas exceptional Class I variants were defined as those that may result in some CFTR protein synthesis. Among the 1033 Class I variants listed, Class I variants were considered exceptional if the variants exhibited one or more or the following characteristics: variants known or predicted to result in splicing defects, potentially leaving a residual transcript and a rescuable protein^20,21; variants located in the last exon or intron of CFTR; T to C substitutions at the +2 position of canonical splice sites; variants for which the clinical data in CFTR2 or in CFTR-France indicate there may be a residual function; variants known or possibly resulting in in-frame exon deletions, except those coding for a part of the protein where CFTR modulators bind; and variants resulting in in-frame exon duplications.

Statistical analysis

Data are presented as n (%), median (IQR), or mean (95% CI), as appropriate. Comparisons of SCC, ppFEV₁, and bodyweight before initiation of ETI and on ETI were conducted using the non-parametric Wilcoxon's matched-pairs signed rank test. All analyses were conducted using Prism 10.03 (GraphPad).

Role of the funding source

Funding sources had no role in data interpretation or analysis, nor in the writing or the decision to submit this manuscript.

Results

The French compassionate programme started on May 19, 2022, and by March 26, 2025, a total of 652 people with CF without an F508del CFTR variant had been screened for inclusion in the programme. Of these, 209 participants had two Class I CFTR variants. Forty-six participants (see CFTR genotypes in Supplementary Table S1) did not receive ETI for the following reasons: 42 harboured two Class I CFTR variants already shown to be non-responsive to ETI in ≥3 participants within the French compassionate programme; three harboured two Class I variants of which at least one has been shown to be non-responsive in 1 or 2 participants within the French compassionate programme; one with two Class I variants of which one was not present in the programme also did not receive ETI. One hundred and sixty-three participants with two Class I CFTR variants received ETI for at least 4–6 weeks: 155 (95%) were considered as non-responders by the centralized adjudication committee, whereas 8 (5%) were considered as responders. A flow chart is presented in Fig. 1.

Fig. 1.

Flow chart.

Aggregated data showing characteristics of responders and non-responders prior to ETI and after 4–6 weeks of ETI are presented in Table 1. Individual data of the 155 non-responders are presented in Supplementary Table S2 and individual data of the 8 responders prior to ETI and 4–6 weeks following initiation of ETI are presented in Table 2. Fig. 2 shows the changes in SCC and ppFEV₁ within 4–6 weeks following ETI initiation in responders and non-responders. Responders showed significant decrease in SCC with a mean difference between prior to and with ETI -18.6 mmol/l (95% CI −28.0 to −7.3; p = 0.055; n = 8), whereas no difference was found among non-responders (mean difference −1.0 mmol/l, 95% CI −3.4 to 1.3; p = 0.12; n = 155). Responders also showed significant increase in ppFEV₁ with a mean difference 11.5 points (95% CI 4.2–18.8; p = 0.0078; n = 8) whereas non-responders showed minimal, yet significant, increase in ppFEV₁ (mean difference 1.7 points, 95% CI 0.4–3.0; p = 0.0073; n = 148; data missing in 7).

Table 1.

Changes in SCC, ppFEV₁, and body weight between initiation and with ETI in 163 pwCF with two Class I variants.

	Non-responders n = 155		Responders n = 8
	Values	n	Values	n
SCC (mmol/L)
Prior to ETI	102 [95; 110]	154	93 [78; 104]	8
With ETI	101 [95; 108]	152	71 [55; 92]	8
Mean absolute change (95% CI)	−1.0 (−3.4; +1.3)	151	−18.6 (−28.0; −7.3)	8
SCC with ETI
≥60 mmol/l, n (%)	152 (100%)	152	6 (75%)	8
30–59 mmol/l, n (%)	0	152	2 (25%)	8
<30 mmol/l, n (%)	0	152	0	8
Missing values	3	3	0	0
Decrease in SCC ≥20 mmol/l with ETI
n (%)	8 (5.3%)	151	4 (50%)	8
Missing values	4	4	0	0
ppFEV1
Prior to ETI	61.5 [42.0; 81.3]	154	59.0 [33.3; 86.0]	8
With ETI	64.5 [47.0; 83.8]	148	77 [47.3; 99.8]	8
Mean absolute change (95% CI)	+1.7 (+0.4; +3.0)	147	+11.5 (+4.2; +18.8)	8
Missing values	7	7	0	0
Absolute increase in ppFEV1
≥5% predicted, n (%)	41 (27.9%)	147	5 (62.5%)	8
≥10% predicted, n (%)	19 (12.9%)	147	5 (62.5%)	8
Missing values	8	8	0	0
Weight (kg)
Prior to ETI	46.5 [35.7; 55.8]	155	56.7 [43.1; 72.5]	8
With ETI	47.0 [36.0; 56.0]	153	57.3 [44.0; 74.8]	8
Mean absolute change (95% CI)	+0.6 (+0.3; +0.8)	153	+2.2 (+0.7; +3.6)	8

CI: confidence interval; ETI: elexacaftor-tezacaftor-ivacaftor; ppFEV1: percent predicted forced expiratory volume in 1 s; SCC: sweat chloride concentration.

Table 2.

Individual data of the 8 participants with two Class 1 variants considered to be responders to ETI.

Patient	CFTR variant #1 (Probably responsive to ETI)	CFTR variant #2	Modulator at initiation	Pancreatic status	Sweat chloride concentration (mmol/L)		percent predicted FEV1 (%)		Weight (kg)		Cough and sputum	Decision to continue ETI
					Prior to ETI	With ETI	Prior to ETI	With ETI	Prior to ETI	With ETI	With ETI
1c	E831Xa	W1282X	None	PS	98	69	86	88	59.5	60.5	Disappeared	Yesb
2c	E831Xa	W401X	None	PS	76	68	28	40	47	49	Decreased	Yes
3c	875+1G > A	3629delT	None	PS	83	51	49	51	73	75	Decreased	Yes
4d	CFTRdup1-3	W846X	None	mild PI	62	41	128	131	41.9	42.3	Disappeared	Yesb
5c	4374+1G > A	3747delC	None	PI	121	137	64	90	54	54	Disappeared	Yesb
6c	4374+1G > A	4374+1G > A	None	PI	88	73	28	46	25	30	Decreased	Yes
7d	1716+2T > C	1078delT	None	PS	99	74	54	66	71	74	Disappeared	Yesb
8c	4382delA	3121-1G > A	None	mild PI	105	98	86	103	86	90	Disappeared	Yes

PS: pancreatic sufficient (fecal elastase ≥200 μg/g); mild PI: mild pancreatic insufficiency (fecal elastase [50; 200]; PI: pancreatic insufficient (fecal elastase <15 μg/g).

^aEMA-approved.

^bThis decision was made after prolongation of the initial ETI trial by 2 additional months.

^cPreviously published.⁸

^dPreviously unpublished.

Fig. 2.

Comparison of sweat chloride concentration (left panel) and percent predicted forced expiratory volume in 1 s (ppFEV₁) (right panel) prior to ETI initiation and with ETI treatment in 163 pwCF with two Class I variants. Data are grouped according to non-responder/responder status as determined by the centralized adjudication committee. Data were analyzed using the Wilcoxon matched-pairs signed rank test. Data are presented as median, Interquartile range, 10–90th percentiles with outliers.

Next, we examined which of the Class I variants were ETI-responsive in the 8 pwCF characterized as responders. When a participant is classified as responder, it implies that at least one of the two CFTR variants is ETI-responsive. Of the 13 variants harboured by the 8 responders with two Class I variants, three variants (W846X [c.2538G > A], W1282X [c.3846G > A], 1078delT [c.948del]) were already characterized as non-responsive in ≥3 participants in the French compassionate programme.⁸ Based on these findings, E831X (c.2491G > T), CFTRdup1-3 (c.-6186_273 + 507dup), and 1716+2T > C (c.1584+2T > C)—all found in trans with one of the aforementioned non-responsive variants in at least one patient (Table 1)—were considered as probably responsive to ETI. Additionally, 4374+1G > A (c.4242+1G > A) was present in homozygosity in one patient, implying that this variant was probably responsive to ETI, also consistent with ex vivo functional tests.²² The variants 4382delA (c.4251del) and 875+1G > A (c.743+1G > A) are associated with milder phenotypes in the CFTR2 and CFTR-France databases, suggesting that they likely result in residual CFTR protein function and could be responsive to ETI. The other variants carried by the patients, W401X (c.1203G > A; a nonsense variant), 3629delT (c.3497del) and 3747delC (c.3615del; frameshift variants) and 3121-1G > A (c.2989-1G > A; a canonical splicing variant) are predicted to result in no CFTR protein and thus to be non-responsive to ETI. Thus, six Class I variants were categorized as probably responsive to ETI in the French compassionate programme: E831X and 4374+1G > A (each present in two participants) and 1716+2T > C, 4382delA, 875+1G > A, and CFTRdup1-3 (each present in one participant).

Next, we examined all potential Class I variants reported in the CFTR2 and CFTR-France databases. Among 1033 potential Class I variants, 955 were considered true Class I variants, which are shown or suspected to result in no CFTR protein (Table 3 and Supplementary Table S3). One hundred and eight of these variants were studied in the French compassionate programme: 23 have been characterized as non-responsive (i.e., present in trans with a non-responsive variant in ≥3 non-responders within the French compassionate programme) and 85 as probably non-responsive (i.e., present in trans with a non-responsive variant in 1 or 2 non-responders within the French compassionate programme, see Supplementary Table S3).

Table 3.

True Class I variants known or expected to produce no CFTR protein and be non-responsive to ETI.

Nonsense	Q2X	W202X	W401X	E585Xb	R785X	S1037X	L1253X
	K14X	W216X	E402X	E588X	R792Xa	Q1038X	L1254X
	W19X	L218X	E407X	K598X	Q799X	Q1042X	S1255X
	G27X	Q220Xb	Q414X	S631X	R810X	E1044X	E1266X
	Q30X	C225X	S434Xa	Q634X	L812X	E1046X	W1274X
	Y38X	Q237X	K442X	G646X	Q814X	L1059X	Q1280X
	Q39X	Y247X	Q452X	Q652X	E815X	W1063Xa	Q1281X
	K52Xa	Q250X	S466Xb	E656X	E822X	Q1071X	W1282Xb
	E54X	E257X	E479X	R657X	E826X	W1089Xa	G1287X
	E56X	Q270X	S489X	S660X	E827X	Y1092X	Q1291X
	W57Xa	Y275Xa	Q493Xa	E664X	K830X	W1098Xb	K1302X
	E60X	C276X	W496Xa	G673X	C832X	Q1100X	Y1307X
	K68X	W277X	E504X	W679X	W846Xb	R1102X	E1308X
	R75Xa	E279X	Y517X	Q685X	Y849X	E1104Xb	Q1309X
	W79X	R289X	C524X	Q689X	R851Xa	R1128X	W1310X
	Y84X	Q290X	Q525Xa	E692X	Y852X	Q1144X	Q1313X
	G85X	E292X	E527X	R709Xa	L867X	W1145X	W1316X
	L88X	Y304X	E528X	K710Xa	W882X	R1158Xa	Q1330X
	Q98X	L320X	S531X	Q715X	Q890X	R1162Xb	K1351X
	L101X	K329X	K536X	K716X	S912X	K1165X	Q1352X
	G103X	G330X	G542Xb	L719X	Y913X	S1178X	E1371X
	R104X	Q353X	G550X	Q720X	K946X	Y1182X	Y1381X
	Y109Xa	W361X	Q552X	E730X	K951X	Q1186X	Q1382X
	K114X	Y362X	R553Xb	L732X	S962X	S1196Xa	Q1390X
	Y122Xb	Q372X	R555X	G745X	K978X	W1204Xa	C1400X
	Q151X	Q376X	Y563X	R764X	Q996X	S1206X	E1401X
	L159X	Q378X	L568X	Q767X	G1003X	Q1238X	E1409X
	L165X	E379X	Y569X	S776Xa	L1011X	L1243X	C1410Xa
	Q179X	K381X	L570X	Q779X	Q1012X	G1247X	Q1411X
	E193X	E384X	Y577X	Q781X	Q1035X	S1248X	Q1412X
	G194X	T388X	L581X
Frameshift	c.4delC	663delT	1289insTA	c.1753delG	2522insC	3090del4	3732delA
	156insG	663insT	1288insA	1918delGC	2556insAT	3089insTC	3737delA
	c.40_44delAAACT	675del4	1291delTT	1924del7	2557delT	3095insT	3747delC
	174delA	675del14	1294del7	1932delG	c.2433_2437delinsATA	3126delA	3750delAG
	175delC	680delT	1309delG	c.1807delG	2567delTa	3129del4a	3750delA
	c.43dupC	c.551_555delTTTCC	c.1190dupT	1942del17	2582delGa	3130delA	3755delG
	181_182dup	690delC	1340delA	1978dupA	2585delT	3132delTG	3755dupG
	c.49_50delTT	c.560delA	1343delG	1978delA	2586-2687insT	3139delG	c.3635delT
	182delT	708delT	c.1219delG	c.1853_1863del	2594delGT	3143delCa	3789insA
	175insT	713delGA	1353delA	2005delTA	c.2467_2470delGAAA	3152delT	3791delCa
	183delC	c.583delC	1366delG	2003del8	2603delT	3154delGa	c.3678delA
	c.71_72delTGinsA	733delGa	1367delC	2025dupA	c.2489_2490insA	3165dupA	3821delT
	218insA	c.604_605delTG	1367del5	2026_2027delGAa	c.2493delG	3171insC	3840delT
	c.88_89delCA	746insC	c.1244delA	2036delAa	2634insT	3171delC	3847delA
	241delATa	749delT	1380insTa	2043delG	2634delTa	3200_3204delTAGTG	3856delC
	c.142_145delAATC	c.650_659del	c.1262delC	2053insTA	c.2443del	3213-3214insTa	3876delA
	c.147_150delATCT	840delT	1429del7	2055del9>A	2640delT	3238delA	3878delG
	295ins8	840insT	1434delA	c.1970delG	2655del26	Q1042TfsX5	3886insA
	284delA	845_846insA	c.1312dupA	2104insA	c.2538delG	3270delAa	3889dupT
	300delA	L240X (c.714del)	1448dupCa	2105-2117del13insAGAAA	2672delA	3293delA	3892delTT
	306delTAGAa	849delG	1461ins4	2109-2118del10	2686dupT	3312delAa	3898insC
	305insT	855del22	D443fs	2113delA	c.2556dupT	3320ins5	3905insTa
	306insA	887delinsGCTGGGAAGAT	1460delAT	2114delT	2694delT	3323_3324insTTTTAAGCTTAAAAGG c.3199delG	3905delT
	308insA	892delA	1465_1466insTAAT	2118del4	c.2573delG	3349insT	3940delG
	317insC	896delT	1471delA	2118del14	2708del13	3359delCTCTG	3944delGT
	354_355delGCinsA	905delGa	1474delA	2132delAC	2711delTa	3359delC	3959delC
	360delT	907delCins11pba	c.1344dup	2143delTa	2721del11	3359delCT	3960-3961delA
	365-366insT (359insT)a	907delCins29	1491-1500del	c.2032_2033delTC	2723delTT	c.3231_3232delGT	3967delTT
	366insC	909delT	1497delGG	2175insA	2732insA	3395dupA	4006delA
	c.234delC	935delA	1498delG	2176insC	2737delA	3396delC	4015delA
	c.243delT	936delTA	1504delG	c.2045delC	2747delC	3422del16	4010del4
	379-381insT	c.811delT	c.1375_1385del	2183AA > Gb	c.2637_2644del	3425delG	c.3883_3884insG
	394delTTb	954delA	1540del10	2183delAA	2771_2772dupTG	3447delG	4016insTa
	c.264_268delATATT	977insA	1548delG	2184insAa	2777insTG	3453delT	c.3889delT
	415insA	982delA	1556delT	2184delAa	2828delG	c.3321dup	4022insT
	435insA	991del5a	1565delCA	2184del4	2837delG	3454delG	c.3893delG
	440delGa	c.865_869delAGACA	1571delG	2185insC	c.2732_2733insA	c.3322_3323delGT	4040delAa
	442delA	1006_1007delGA	1576insT	c.2053delC	c.2733insA	3456delC	4040dupA
	444delA	1027delG	1601delT	c.2053_2054insAA	2869insGa	c.3325delA	4048insCC
	c.324delC	1037insA	1601delTC	2189CT > A	2875_2877delGTGinsA	c.3344_3345insA	4064-4065delinsAATATG
	457TAT > G	1040del4	1609delCAa	2193ins4	c.2745_2746delGT	3497delC	4089ins4
	458delAT	c.912delCinsGG	c.1486delT	2215delG	2896insAGa	c.3380_3383del	4089delA
	464delC	1058delC	1660delG	c.2089delA	2907delTT	3516del5	4108delT
	c.353delC	c.937_938delTC	c.1530_1531delTT	2221insA	2909delT	3521del14	4120delCA
	489delCa	c.942delG	1675_1687del13	2222delG	c.2789delG	3528delC	c.3999delG
	499dupC	1078delTb	1677delTAb	c.2148delG	2935del11	3532AC > GTA	c.4028delG
	503delGa	1091delT	c.1547_1548delGA	2290del16	2937_2942delinsTCAGA	3539del16	4160insG
	c.381_382dup	c.972delC	c.1573delC	2307insA	2942insTa	c.3411_3414delGAAT	4165delGT
	519delT	1112delT	1706del17	2335delA	2948delA	3556insAGTA	p.S1347PfsX13
	525delT	c.982delA	c.1581dupA	2347delGa	c.2818_2831del	c.3426_3427insGTAA	c.4036dupC
	526_527delAT	1119delA	c.1608delA	2372del8	2949del5	3586_3587delCAa	4168delCTAAG
	538insAC	c.991_995del	1749insTA	2380_2387del; S753Sa	2951insA	c.3477delT	4172delGC
	541delC	1134delGa	1759delG	2380_2387del; S753Sa	2954delT	3613AGCCGA > GG	4177delG
	541del4	1138insG	1774delCT	c.2250delT	2957delT	3617delGA	4197_4198delCT
	542del7	1154insTC	1782delA	c.2261delT	2967delG	3622insT	4203delT
	547insTA	1157insTA	1784delG	2406_2407delinsT	c.2839delA	c.3495delG	4203TAG > AA
	556delA	1161delC	1784insATCAT	2409delC	2975delT	3629delT	4209TGTT > AA
	557delT	1185delTC	1787delA	2423delG	2991del32	c.3524delC	c.4078delG
	565delC	1200_1219del20	1802delC	2429delG	3007delGa	c.3525_3537del	4218insT
	574delA	1199delG	1806delA	2435insC	c.2879_2882delCTAT	3659delCb	4222delG
	c.450delG	1204_1205delGT	1807delG	2456delAC	3011delC	3662delA	4237-4242delinsAGAA
	582insG	1212delA	1813insC	2466delC	3012delT	3667ins4	4259del5
	583delC	1213delTa	1824delA	c.2337delA	3015_3018dupGTCA	3667del4	4271delCa
	593insT	1215delG	1833delT	2472_2478del7	3028delA	c.3539_3554del	4279insA
	602del14	c.1084_1088dup	c.1708_1712delTTATT	c.2341delC	3029delC	3695delC	c.4163_4167delTAAAA
	604insA	1221delCT	1845delAG/1846delGA	2481-2482insT	3031-3032delinsA	c.3569_3570delTT	c.4187delC
	605insT	c.1115delA	1857delT	c.2357dupA	c.2909_2924dup16	3724delG	4301delA
	c.488delA	1249insA	c.1725_1727delinsAT	2505delA	3051_3052insAlu121bp	3730A > TCT (3730delAinsTCT)a	4326delTC
	624delT	1259insA	1870delG	2510delAA	3056delGA	3730_3731AA > Ga	4332delTG
	630delG	1262delA	1874_1875insTT	2512delG	3061insA	3731-3732AA > G
	654del5	1288insTA	1874insTa
Canonical splice site	185+1G > Ta	621+1G > A	1002-2A > C	1524+1G > A	1898+1G > T	3041-1G > A	3500-2A > G
	185+2T > G	621+1G > Tb	1248insATCAA	1525-2A > G	1898+2delT	3041-1G > C	3500-2A > T
	186-2A > G	621+2T > Ga	1248+1G > A	1525-1G > Aa	1898+2T > A	c.2982_2988+2delCATCCAGGT	3500-1G > A
	186-1G > A	622-2A > C	1248+1G > C	1525-1G > C	1899-2A > G	3120+1G > Ab	3600+1G > A
	296+1G > A	710_711+5del7	1248+1G > T	1525-1G > T	1899-1G > A	3120+1G > C	3600+1G > Ta
	296+1G > C	710del4	1248+2T > A	1710del17bp	2622+1G > Ab	3121-2A > C	3601-2A > C
	296+1G > T	711+1G > Tb	1249-1G > A	1716+1G > A	2622+1G > T	3121-2A > G	3601-2A > G
	296+2T > A	712-2A > C	1341+1G > A	1716+1G > T	2623-2A > G	3121-2A > T	3601-1G > A
	296+2T > G	712-2A > G	1341+1G > C	1716+2delT	2623-1G > C	3121-1G > A	3601-1G > C
	297-2A > C	712-1G > T	1341+1G > T	1717-2A > G	2751+1G > A	3121-1G > T	3601-1G > T
	297-2A > G	852del22	1341+2T > A	1717-1G > Ab	2751+2T > A	3271delGG	3849+1G > A
	297-1G > A	875insTACA	1341+2T > G	1717-1G > T	2752-2A > G	3271+1delG	4006-2A > G
	405+1G > A	875+2T > A	1342-2delAG	1811+1G > A	2752-1G > T	3271+1G > A	4006-1G > A
	405+2T > G	876-2A > G	1342-2A > C	1811+1G > Ca	2787del16	3271+1G > C	4095+1G > A
	406-2A > C	994del9	1342-1delG	1812-2A > C	2790-2A > G	3271+1G > T	4095+1G > C
	406-2A > Ga	1001+1G > C	1342-1G > A	1812-1G > Aa	2790-1G > C	3272-1G > A	4095+1G > T
	406-1G > A	c.869 + 1_869+4delins8	1342-1G > C	1812-1G > C	2790-1G > T	3499+1G > A	4095+2T > A
	406-1G > C	1001+2T > A	1342-1G > T	1898+1G > A	3040+1G > Aa	3499+1G > T	4096-1G > A
	406-1G > T	1001+2T > G		1898+1G > C	3040+1G > T	3499+2T > A	4268+2T > G
Exon deletion/duplication	CFTRdelePr-1	CFTRdele2,3,10	CFTRdele4-6ains6	CFTRdup6b-10	CFTRdele11-14b	CFTRdup14b-17b	3413_3499 + 268del355bpins6bpa
	CFTRdelePr-3	CFTRdele2-4a	CFTRdele4-7	CFTRdup6b-16	CFTRdele11-15,17a,17b	CFTRdele14b-20	CFTRdele17b,18
	CFTRdelePr-9	CFTRdup2-4	CFTR50kbdel	CFTRdele7	CFTRdele11-16ins35	CFTRdele15	CFTRdup17b-18
	CFTRdelePr-14a	CFTRdele2-6b	CFTRdele4-7,11-18	CFTRdele7,8	CFTRdele11-18	CFTRdele15,16	CFTRdele18
	CFTRdele1	CFTRdele2-7	CFTRdele4-7,12-18	CFTRdele7,9	CFTRdele12,13,16	CFTRdele16,17a	CFTRdele18-20
	135del120ins300	CFTRdele2-8	CFTRdele4-8	CFTRdele7-9a	CFTRdele12-18	CFTRdele16-17ba	CFTRdele18-24
	CFTRdup1	CFTRdele2-9	CFTRdup4-8	CFTRdele7-10	CFTRdele12-14a	CFTRdele16-18	CFTRdele19,20
	CFTRdele1-4	CFTRdele2-10	CFTRdele4-8,12-21	CFTRdele8,9	CFTRdele13	CFTRdup16-18	CFTRdele19-21
	CFTRdele1-9	CFTRdele2-22	CFTRdele4-10	CFTRdup8-10	CFTRdele13,14a	CFTRdele16-20	CFTRdele19-24
	CFTRdele1,10	CFTRdele3	CFTRdup4-10	CFTRdele9,10	CFTRdele14a-15	CFTRdup16-20	CFTRdele19-23
	CFTRdele1-10	CFTRdup3	CFTRdele4-11	CFTRdup9-21	CFTRdele14a-17b	CFTRdup16-22	CFTRdele20-23
	CFTRdele1,11-24	CFTRdele3-10,14b-16a	CFTRdup4-19	CFTRdup10-12	CFTRdup14a-19	CFTRdele17a	CFTRdele22
	CFTRdele1-24	405 + 7982del18652	CFTRdele5,6a	CFTRdele10-14b	CFTRdele14b	c.2989-908_3085delinsGACAG	CFTRdele22,23
	CFTRdup1-24	CFTRdele4-6b	c.613_870-1547del	CFTRdele11	CFTRdele14b,15a	CFTRdele17a,17ba	CFTRdele22-24
	CFTRdele2ins182a	CFTRdele4	CFTRdup6a,6b	CFTRdele11,12	CFTRdele14b-17ba	CFTRdele17a-18b	CFTRdele23
	CFTRdele2,3b	CFTRdele4,5,7,10	CFTRdup6b,7	CFTRdup11-13		CFTRdele17b	CFTRdele23,24
		CFTRdele4-6a
Start-loss	124del23bp	M1I	M1R	M1K	M1Ta	M1V

Dele: deletion; Dup: duplication; Pr: CFTR promoter region.

A number of variants are written following HGVS rules (« c. », e.g., c.4delC) as they were described only by their HGVS names and not legacy names.

^aVariants harboured by 1–2 patients in the French compassionate programme in trans with a non-responsive variant and who were non-responders to ETI.

^bVariants harboured by ≥ 3 patients in the French compassionate programme in trans with a non-responsive variant who were non-responders to ETI.

A list of 78 “exceptional” Class I variants, which are shown or suspected to result in the production of some CFTR protein, is presented in Table 4 and Supplementary Table S3). Of these, six variants were probably responsive to ETI as they were present in 1–2 pwCF responders to ETI in the French Compassionate Programme, whereas five variants were probably non-responsive to ETI as they were present in 1–2 pwCF non-responders to ETI in the French compassionate programme.

Table 4.

Exceptional Class I variants, which may be expected to produce CFTR protein.

Variants probably responsive to ETI within the French compassionate programme
Nonsense	E831Xa
Frameshift	4382delA
Canonical splice site	875+1G > A	1716+2T > C	4374+1G > A
Exon deletion/duplication	CFTRdup1-3
Variants probably non-responsive to ETI within the French compassionate programme
Canonical splice site	3850-1G > A	4005+1G > A	4375-2A > C	4374+1G > T
Exon deletion/duplication	CFTRdele19
Variants with no data on ETI responsiveness in the French Compassionate Programme
Nonsense	S4X E33X	E92X Q207X	W356X E514X	K688X E1418X	Y1424X S1455X	E1473X Q1476X
Frameshift	681delC 2075delA	2108delA 3041delG	4168delCTAAGCC 4375_4376insCTGT	4384delG 4428insGA	4433insGA 4482del	4506insC c.4399_4477del
Canonical splice site	185+2T > C 296+2T > C 621+2T > C 622-1G > A 622-1G > C	622+1G > T 711+2T > C 875+1G > C 875+2T > C 1002-2A > G	1248+2T > C 1524+1delG 1811+2T > C 1898+2T > C	2622+2T > C 2751+2T > C 3271+2T > C c.3368-2dup 3499+2T > C	3600+2insT 3600+2T > C 4005+1G > T 4005+2T > C	4374+2T > C 4375-2A > G 4375-1G > A 4375-1G > T
Exon deletion/duplication	CFTRdele2 CFTRdup2 CFTRdele6b	CFTRdele8 CFTRdele9 CFTRdele10	CFTRdele12 CFTRdele14a CFTRdup16,17a	CFTRdup19 CFTRdele20 CFTRdele21	CFTRdup22 CFTRdup22,23 CFTRdup22-24	CFTRdele24

Dele: deletion; Dup: duplication; Pr: CFTR promoter region.

^aEMA-approved.

Discussion

In the present study, we first analysed data from pwCF exposed to ETI within the French compassionate programme. This reanalysis was limited to 163 participants with two Class I CFTR variants who received ETI within the programme as (A) pwCF harbouring these genotypes are excluded from the recent EMA label expansion for ETI, which was released in April 2025, and (B) no large-scale data existed on the effects of ETI in pwCF with two Class I variants. Our data showed that over 95% of pwCF with two Class I variants were considered as non-responders by the French compassionate centralized adjudication committee. We however found that 5% of pwCF harbouring two Class I variants, including at least one variant with exceptional characteristics (i.e., predicted to result in some CFTR protein synthesis), were categorized as responders to ETI. These data underscore the need to distinguish true Class I variants from known or potential exceptions to Class I and to establish lists of CFTR variants responsive and non-responsive to ETI. This will ensure that ETI is used in responders and not used in non-responders and that access to ETI is not denied to patients with exceptional Class I variants.

As the expanded French compassionate programme provided access to a 4–6 weeks trial of ETI in all pwCF with no F508del variant aged 6 years and older, regardless of CFTR genotypes, the present study represents the largest clinical experience of ETI in pwCF with two Class I variants. Because Class I variants are predicted to result in no CFTR protein, our data largely confirmed the prediction that pwCF with two Class I variants do not show clinical response to ETI, a finding observed in over 95% of participants in this study. It has long been known that E831X is associated with a milder phenotype, including CFTR-related disorders, and results in a residual functional CFTR protein, notably due to alternative splicing at a tandem acceptor splice site²³ and is therefore not a true Class I variant. E831X has been predicted to respond to ivacaftor based on data obtained in cultured cells,²⁴ and has been approved by the EMA for the use of ETI based on in vitro data; it is also FDA-approved for ETI treatment. Our findings confirm these predictions in the clinical setting for E831X and extend these findings to at least five additional Class I variants: 4374+1G > A, 1716+2T > C, 4382delA, 875+1G > A, and CFTRdup1-3. Interestingly, each of these responsive Class I variants has exceptional characteristics, predicting the synthesis of CFTR protein (see Table 5 for details). Of note, six out of the eight responders were pancreatic sufficient (fecal elastase ≥200 μg/g) or had mild pancreatic insufficiency (fecal elastase 50–200 μg/g), suggesting a residual CFTR function. The two participants with the splicing variant 4374+1G > A were, however, pancreatic insufficient.

Table 5.

Mechanisms by which variants assumed to belong to Class I proved to be likely responsive to ETI in the French Compassionate Programme.

Mechanism	Variant category	Variants
Variants known or predicted to result in splicing defects which leaves a residual transcript and a rescuable protein	Nonsense, frameshift	E831X
Variants located in the last exon or intron which may be associated with a functional protein and not lead to nonsense mediated decay	Any	4382delA, 4374+1G > A
Canonical splice site +2T > C variants which may give rise to normal transcripts	Canonical splice site	1716+2T > C
Variants for which the clinical data in CFTR2 or CFTR-France indicates there may be residual function	Any	E831X, 4382delA, 875+1G > A, CFTRdup1-3

The study was based on a sub-analysis of published data from the French compassionate programme,⁸ complemented by previously unpublished cases as the programme is ongoing. For a limited number of Class I variants (n = 23), the absence of response to ETI was based on ≥3 cases, providing confidence that these variants are non-responsive to ETI. For other Class I variants (85 classified as probably ETI-non-responsive, and six classified as probably ETI-responsive) clinical evidence was limited to one or two participants in the French compassionate programme, leading to a lesser degree of confidence. For a large number of Class I variant, no patient had received ETI, consistent with previous studies which showed that over 1200 variants are present in fewer than 5 patients worldwide.⁵ Thus, many variants may not have been present in France or may have been found only in trans with responsive variants (e.g., F508del), precluding any conclusion of their response to ETI. Notably, response to ETI may be affected by adherence to therapy, dietary food intake and drug–drug interactions. Although adherence was not directly monitored during individual trials, it was likely high in motivated participants in the French compassionate program. All patients were instructed that ETI should be taken with fat-containing food and possible drug–drug interactions were reduced by systematically stopping drugs that may interfere with ETI prior to the individual treatment trial.

Responsiveness to ETI relied on multiple criteria, including clinical manifestations (daily symptoms, exacerbation during the trial period), SCC, ppFEV₁, and CT scans when available. Since biomarkers (e.g., SCC and ppFEV1) were factors contributing to response categorization, their summary statistics may be expected to be biased relative to the corresponding true parameters. An important aspect, already mentioned in our previous description of the French compassionate programme, is that decisions were made based on multiple biomarkers, as a single biomarker with a specific cut-off value is often not sufficient to establish responsiveness or non-responsiveness. Integrating all numerical biomarkers and clinical data together helped minimize the risk of bias. Daily symptoms are informative when the patient stops coughing and producing sputum, but is relatively subjective. ppFEV₁ usually increases when the patient is a responder, but the magnitude of the increase can be variable, depending on age and baseline ppFEV1 prior to initiation.²⁵ Additionally, ppFEV₁ may increase following better adherence to airway clearance techniques or an antibiotic course; this was the case for 41/155 (27.9%) participants with two true Class I variants that did not show any other evidence of response to treatment. SCC is informative when a large decrease occurs following ETI initiation and the value under ETI is below 60 mmol/l. However, we previously described CFTR variants (e.g., N1303K [c.3909C > G], 2789+5G > A [c.2657+5G > A] and R334W [c.1000C > T]) responsive to ETI that do not show a decrease in SCC following ETI initiation. Only 4/8 (50%) of the responders in the present study had decrease in SCC of more than 20 mmol/l, suggesting that some of these exceptional Class I variants may also not show a decrease in SCC, a finding that will require confirmation in future studies.

Before the recent expansion of the ETI label by the EMA in April 2025, approval by regulatory agencies around the world has been based on the presence of selected CFTR variants. The lists of approved variants were based on results of clinical trials (e.g., for F508del) or on in vitro data (e.g., using Fisher Rat Thyroid cells transfected with non-F508del, often rare, CFTR variants). Real-world administration of ETI, including in the French compassionate programme, has shown that many variants not present in these lists could prove responsive to ETI, although nonsense variants were generally found non-responsive.^7,8 The EMA label introduced for the first time a negative selection of variants as it suggested that ETI could be tested in the clinic in pwCF aged 2 years and older “who have at least one non-Class I mutation in the CFTR gene.” The inclusive definition of Class I variants (nonsense, canonical splice site variants, small insertions or deletions that result in a premature termination codon (frameshift), exon deletions or duplications and start-loss variants), although simple, is too broad. As shown in the present study, Class I is heterogeneous and some exceptional Class I variants with particular characteristics are responsive to ETI, as they result in the synthesis of a residual functional CFTR protein and therefore do not behave like true Class I variants.

The criteria used in this study to identify exceptional Class I variants in the CFTR2 and CFTR-France databases are based on current understanding of CFTR biology and may not be sufficient to identify all variants that allow CFTR protein production. Therefore, we must allow for the possibility that some variants characterized as true Class I variants in this manuscript may be ETI-responsive, though this is likely a small minority, if any. Likewise, identification of a Class I variant with exceptional characteristics does not guarantee a clinical response to ETI; indeed, five patients in the French compassionate programme harboured exceptional Class I variants but were considered as non-responders. Just as Class I variants on the whole are not a homogeneous group, nor are exceptional Class I variants, with some having a greater likelihood of ETI response than others due to underlying molecular mechanisms of disease. Variants known or predicted to result in splicing defects, leaving a residual transcript and a potentially-rescuable protein,^20,21 were identified using prediction algorithms and further work is necessary to confirm splicing predictions and whether resulting isoforms indeed lead to rescuable protein, as most have not been studied. It is known that T to C substitutions at the +2 position of canonical splice sites can somewhat be tolerated, giving rise to normal transcription,²⁶ but this tolerance may vary by location in CFTR or due to other factors. Little is known about whether in-frame single exon deletions or single or two-exon duplications will result in functional or rescuable CFTR protein; this also likely varies by exon location and CFTR protein domain 20. Conversely, all Class I variants located in the last exon of CFTR that have been functionally studied have shown production of CFTR protein that is rescuable by modulators; therefore, it is reasonable to conclude that any Class I variant located in this exon will be exceptional. It is beyond the scope of this manuscript to further subdivide this group of 78 exceptional Class I variants into those with a high likelihood of ETI response vs. those with a lower likelihood, but such a study in the future would provide valuable information for prescribers and patients alike. The results reported here and following future work may also inform updates to variant databases such as CFTR2 and CFTR-France, which consider multiple characteristics of and data associated with each variant when assigning an interpretation. Identification of variants that require a more nuanced functional evaluation is crucial for accuracy in overall variant assessment.

While the lists of true and exceptional Class I variants reported here are derived from large datasets, it is recognized that these are not comprehensive. In the case that a prescriber receives a laboratory report identifying an apparent Class I variant not included in this manuscript, it is recommended that the variant be considered for any characteristics that could make it exceptional. This may include assessment of potential effects on splicing, determination of location within CFTR (e.g., exon 27 or a T > C change at the +2 position), and a careful clinical evaluation to determine whether there is evidence of residual CFTR function in the patient (e.g., SCC<85 mmol/l or pancreatic sufficiency) that cannot be attributed to the other CFTR allele. If any evidence for exceptionality is found, a trial of ETI may be warranted at the prescriber's discretion, with the understanding that patient response cannot be predicted. It should also be noted that most exceptional Class I variants are not included in commercial genetic panels due to their rarity (all <0.1% frequency in CFTR2). They are easily detected by next generation sequencing, but this technology is not be available in all clinical settings.

In the present study, we defined true and exceptional Class I variants for the exclusive purpose of helping prescribers to determine potential responsiveness to ETI, regardless of the underlying mechanism allowing CFTR protein production. Previous suggestions were made to divide Class I into two groups called Class I and Class VII²⁷ or sub-class IA and IB,¹⁴ based on mechanism(s) resulting in the CFTR defect. The true vs. exceptional classification is not superimposable with those proposed in previous studies, as we have identified exceptional variants belonging to both the proposed Class I and VII or proposed sub-class IA and sub-class IB.

Future research in this area should (1) interrogate clinical data obtained from patients with Class I variants treated with ETI, as pooled analysis of data from multiple countries may increase the number of patients with each variant and the level of clinical evidence (2) use in vitro models (e.g., Fisher rat thyroid [FRT] cells and inducible pluripotent stem cells [iPSC]) or patient-derived cells (e.g., nasal cells and rectal organoids) to gain knowledge regarding the production of CFTR protein and responsiveness to ETI.

The EMA label is a major step forward as it allows testing ETI in pwCF with ultra-rare variants, which ensures that all pwCF potentially responders to ETI are eligible to a trial of ETI under close medical supervision. It has also some limitations as a very limited number of pwCF with two Class I variants may derive clinical benefit from ETI (eight pwCF in France, all harbouring at least one exceptional Class I variant, representing less than 1/1000 pwCF). Additionally, the label ignores that some selected non-Class I variants (e.g., I507del (c.1519_1521del),⁸ a Class II variant) are also non-responsive to ETI. Whereas the EMA label provides a general guidance for eligibility and access to ETI, treating clinicians should always consider individual genotypes before prescribing ETI as some pwCF within the label may not respond to ETI, whereas some pwCF with exceptional Class I variants may respond to ETI. These findings underscore the relative complexity of providing guidance on ETI-responsiveness in pwCF with ultra-rare variants. It is thus not surprising that a regulatory approval label cannot solve all the individual cases.

The EMA label excluded patients with CF “who harbor two Class I (null) mutations (mutations that are known not to produce CFTR protein),” corresponding to our definition of “true” Class I variants. As “exceptional” Class I variants are “shown or suspected to result in some protein production” they are not excluded from the EMA label. We suggest that future regulatory framework may make the difference between true and exceptional Class I variants for the approval of CFTR modulators.

In conclusion, Class I CFTR variants are generally not responsive to ETI, presumably due to the absence of CFTR protein, which appears necessary for binding of CFTR modulators. However, Class I variant constitute a heterogeneous group in which some exceptional variants could be expected to produce a CFTR protein and thus not to behave as Class I variants. Our study revealed that some of these exceptional Class I variants are probably responsive to ETI, whereas others reveal probably not responsive. Mapping CFTR variants for establishing lists of variants responsive vs. non-responsive to ETI and to other CFTR modulators (e.g., vanzacaftor-tezacaftor-deutivacaftor)²⁸ is important to ensure that all pwCF with at least one responsive variant will benefit from appropriate treatment, without exposing pwCF with two non-responsive variants to the adverse effects of CFTR modulators with no expected benefits.

Contributors

Conceptualization: PRB, EG, KR.

Data curation, formal analysis: all authors.

Funding acquisition: PRB.

Investigation: all authors.

Methodology: all authors.

Project administration: PRB, KR.

Resources, software: all authors.

Supervision: PRB, EG, KR.

Validation and visualization: All authors.

Writing original draft: PRB, EG, JDS, KR.

Writing review & editing: all authors.

All authors had access to the data and were responsible for the decision to submit the manuscript.

Data sharing statement

Data may be requested to the principal investigator, Pierre-Régis Burgel.

Declaration of interests

The authors declare no conflict of interest in relation to this study. PRB declares consulting fees from Astra-Zeneca, Chiesi, GSK, Insmed, MSD, Sanofi, Vertex, and Viatris outside of the submitted work; PRB also declares grants from Vaincre la Mucoviscidose, Société Française de la Mucoviscidose and Filière Maladies Rares MUCO-CFTR for the submitted work. ISG declares grants and consulting fees from Vertex, outside of the submitted work. EG declares fee for lecturing from Vertex. CFTR-France received grants from Vaincre la Mucoviscidose. CM declares consulting fees from Astra-Zeneca, Chiesi, Zambon and support for attending meetings from Boehringer Ingelheim, Chiesi. Sanofi and Zambon. JDS have nothing to declare. KR has nothing to declare. CFTR2 received grants from the Cystic Fibrosis Foundation. NS received grants from Vertex. SS has nothing to declare. CR received consulting fees from Vertex outside of the submitted work; she has unpaid position in the National Commission for NewBorn Screening and Filière de Santé Maladies Rares Muco-CFTR in France.