Submissions for variant NM_000492.4(CFTR):c.2991G>C (p.Leu997Phe)

gnomAD frequency: 0.00208  dbSNP: rs1800111

Total submissions: 29

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000046745	SCV000074758	benign	Cystic fibrosis	2024-02-01	criteria provided, single submitter	clinical testing
Eurofins Ntd Llc (ga)	RCV000078991	SCV000226875	pathogenic	not provided	2016-08-12	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003891433	SCV000304486	likely benign	CFTR-related condition	2022-10-27	criteria provided, single submitter	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
CeGaT Center for Human Genetics Tuebingen	RCV000078991	SCV000493335	pathogenic	not provided	2023-09-01	criteria provided, single submitter	clinical testing	CFTR: PM3:Very Strong, PM2:Supporting, PS3:Supporting
GeneDx	RCV000078991	SCV000589481	uncertain significance	not provided	2018-12-27	criteria provided, single submitter	clinical testing	The L997F variant in the CFTR gene has been reported previously in trans with another pathogenic CFTR variant in individuals with cystic fibrosis and atypical cystic fibrosis, as well as in asymptomatic individuals (Lucarelli et al., 2010; Strom et al., 2011; Schippa et al., 2013). It has been suggested that the presence of the R117L variant in cis with L997F as a complex allele may in part explain the variable phenotype observed in individuals with the L997F variant (Lucarelli et al., 2010). The L997F variant is observed in 59/10,146 (0.58%) alleles from individuals of Ashkenazi Jewish background in large population cohorts (Lek et al., 2016). The L997F variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Functional studies demonstrated that the L997F variant was associated with somewhat reduced chloride transport (VanGoor et al., 2014). We interpret L997F as a variant of uncertain significance.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000078991	SCV000601084	uncertain significance	not provided	2023-08-02	criteria provided, single submitter	clinical testing	The CFTR c.2991G>C (p.Leu997Phe) variant has been reported with other CFTR variants in the published literature in individuals with Cystic Fibrosis (CF) (PMID: 1379210 (1992), 9921909 (1998), 17572159 (2008), 20706124, 21804385 (2011), 23613805 (2013), 27738188 (2016)) and CF-related disorders including pancreatitis (PMID: 10801389 (2000), 18501000 (2008), 20460946 (2010), 23951356 (2013), 29589582 (2018)), bronchiectasis (PMID: 9921909 (1998)) and congenital bilateral absence of the vas deferens (CBAVD) (PMID: 9272157 (1997), 10875853 (2000), 26911355 (2016)). This variant is also found to occur as part of a complex allele p.[R117L; L997F] and is often associated with a more severe phenotype in individuals with cystic fibrosis (PMID: 25910067 (2015)). This variant has also been reported in asymptomatic individuals (PMID: 12014388 (2002), 15857421 (2005)). Functional studies indicated that this variant results in reduction of CFTR chloride transport activity, channel diameter and alters bicarbonate permeability (PMID: 25824995 (2015), 23891399 (2014), 25033378 (2014)). The frequency of this variant in the general population, 0.0099 (115/11590 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000078991	SCV000602993	uncertain significance	not provided	2023-10-27	criteria provided, single submitter	clinical testing	The CFTR c.2991G>C; p.Leu997Phe variant (rs1800111) has been identified in multiple individuals diagnosed with CFTR-related disorders (Bergougnoux 2015, Gallati 2009, Gomez-Lira 2000, Hamoir 2013, Lucarelli 2010, Masson 2013, Pelletier 2010), but case control studies disagree if this variant is enriched in pancreatitis patients (LaRusch 2014, Gomez-Lira 2000). In addition, individuals homozygous for this variant have been reported to be clinically asymptomatic (Derichs 2005, Stanke 2008, Terlizzi 2017). Functional characterization of the variant protein indicates a reduction in the CFTR chloride transport activity (Bergougnoux 2015, Sosnay 2013, Van Goor 2014), but at a level unlikely to cause cystic fibrosis (Sosnay 2013, Strom 2011). This variant is reported in ClinVar (Variation ID: 7229) and is observed in the general population at a frequency of 0.22% (627/282204 alleles, including 3 homozygotes) in the Genome Aggregation Database. The leucine at codon 997 is highly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.625). Due to the conflicting information regarding this variant, its clinical significance cannot be determined with certainty. References: Bergougnoux A et al. Should diffuse bronchiectasis still be considered a CFTR-related disorder? J Cyst Fibros. 2015; 14(5):646-53. PMID: 25797027. Derichs N et al. Homozygosity for L997F in a child with normal clinical and chloride secretory phenotype provides evidence that this cystic fibrosis transmembrane conductance regulator mutation does not cause cystic fibrosis. Clin Genet. 2005; 67(6):529-31. PMID: 15857421. Gallati S et al Cystic fibrosis transmembrane conductance regulator mutations in azoospermic and oligospermic men and their partners. Reprod Biomed Online. 2009; 19(5):685-94. PMID: 20021716. Gomez-Lira M et al. High frequency of cystic fibrosis transmembrane regulator mutation L997F in patients with recurrent idiopathic pancreatitis and in newborns with hypertrypsinemia. Am J Hum Genet. 2000; 66(6):2013-4. PMID: 10801389. Hamoir C et al. Clinical and morphological characteristics of sporadic genetically determined pancreatitis as compared to idiopathic pancreatitis: higher risk of pancreatic cancer in CFTR variants. Digestion. 2013; 87(4):229-39. PMID: 23751316. LaRusch J et al. Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis. PLoS Genet. 2014 10(7):e1004376. PMID: 25033378. Lucarelli M et al. A new complex allele of the CFTR gene partially explains the variable phenotype of the L997F mutation. Genet Med. 2010; 12(9):548-55. PMID: 20706124. Masson E et al. A conservative assessment of the major genetic causes of idiopathic chronic pancreatitis: data from a comprehensive analysis of PRSS1, SPINK1, CTRC and CFTR genes in 253 young French patients. PLoS One. 2013; 8(8):e73522. PMID: 23951356. Pelletier A et al. CFTR gene mutation in patients with apparently idiopathic pancreatitis: lack of phenotype-genotype correlation. Pancreatology. 2010; 10(2-3):158-64. PMID: 20460946. Sosnay PR et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet. 2013; 45(10):1160-7. PMID: 23974870. Stanke F et al. Diversity of the basic defect of homozygous CFTR mutation genotypes in humans. J Med Genet. 2008; 45(1):47-54. PMID: 18178635. Strom C et al. The dangers of including nonclassical cystic fibrosis variants in population-based screening panels: p.L997F, further genotype/phenotype correlation data. Genet Med. 2011; 13(12):1042-4. PMID: 21804385. Terlizzi V et al. Genotype-phenotype correlation and functional studies in patients with cystic fibrosis bearing CFTR complex alleles. J Med Genet. 2017 Apr;54(4):224-235. PMID: 27738188. Van Goor F et al. Effect of ivacaftor on CFTR forms with missense mutations associated with defects in protein processing or function. J Cyst Fibros. 2014; 13(1):29-36. PMID: 23891399.
Counsyl	RCV000046745	SCV000800721	uncertain significance	Cystic fibrosis	2017-03-22	criteria provided, single submitter	clinical testing
Mendelics	RCV000046745	SCV000886143	uncertain significance	Cystic fibrosis	2018-11-05	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000243402	SCV000919167	benign	not specified	2020-11-12	criteria provided, single submitter	clinical testing	Variant summary: CFTR c.2991G>C (p.Leu997Phe) results in a non-conservative amino acid change located in the ABC transporter type 1, transmembrane domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0024 in 254424 control chromosomes in the gnomAD database, including 3 homozygotes. This frequency is not significantly higher than expected for a pathogenic variant in CFTR causing Cystic Fibrosis (0.0024 vs 0.013), allowing no conclusion about variant significance. c.2991G>C has been reported in the literature in patients with a wide range of atypical CFTR-related phenotypes such as bronchiectasis, pancreatitis, hypertrypsinemia, asthma, renal agenesis without a strong evidence of causality (example, Lebecque_2011, Tzetis_2001, Casals_2000, Padoan_2002); it is also found in ~ 1% of normal alleles from various studies. Of note, two homozygote individuals, one completely unaffected (Derichs_2005) and one only affected with allergic bronchopulmonary aspergillosis (ABPA) (Lebecque_2011) have been reported. The variant has also been found to be in cis with other CFTR deleterious variants such as deltaF508 (Fanen_1992), a large deletion spanning exons 2-9 of the CFTR gene (Schneider_2007, Strom_2011) and with R117L (Lucarelli_2010, classified as likely pathogenic) in CF patients supporting a benign outcome. Lastly, the variant has also been reported as having been co-inherited with a disease causing deletion spanning the entire SPINK1 gene in one family segregating with chronic pancreatitis (Masson_2007, cited in Bombieri_2011) supporting an alternative molecular basis of disease. These data indicate that the variant is unlikely to be associated with CF or any of its related variably expressive disease phenotypes. Reputed databases such as CFTR2 cite this variant as not disease causing (Sosnay_2013). In addition, functional studies suggest the variant could play a role in bicarbonate permeability relevant to organs in which CFTR is used for bicarbonate secretion (LaRush_2014) and has significantly reduced chloride conductance (Van Goor_2013), however the in vivo impact of these functional defects are unknown. Twelve clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments, at-least two other submitters report a benign/likely benign outcome. Based on the evidence outlined above, the variant in isolation was classified as benign for CF and associated phenotypes.
CFTR-France	RCV001009470	SCV001169565	pathogenic	CFTR-related disorders	2018-01-29	criteria provided, single submitter	curation
Ambry Genetics	RCV000046745	SCV001178980	uncertain significance	Cystic fibrosis	2023-01-12	criteria provided, single submitter	clinical testing	The p.L997F variant (also known as c.2991G>C), located in coding exon 19 of the CFTR gene, results from a G to C substitution at nucleotide position 2991. The leucine at codon 997 is replaced by phenylalanine, an amino acid with highly similar properties. This alteration is known to occur in isolation or as part of a complex allele, p.[R117L;L997F], and it is associated with a range of clinical outcomes (Stanke F et al. J. Med. Genet., 2008 Jan;45:47-54; Lucarelli M et al. Genet Med, 2010 Sep;12:548-55; Strom CM et al. Genet Med, 2011 Dec;13:1042-4; Lucarelli M et al. Mol Med, 2015 Apr;21:257-75; Terlizzi V et al. J. Med. Genet., 2017 04;54:224-235). Some individuals homozygous for p.L997F or compound heterozygous with a second CFTR mutation were reported to be asymptomatic, whereas others had intermediate sweat chloride levels and exhibited CFTR-related disorders, including congenital bilateral absence of the vas deferens, pancreatitis, and bronchiectasis. In contrast, the p.[R117L;L997F] complex allele is associated with a more severe phenotype and has been described in multiple homozygous or compound heterozygous individuals with elevated sweat chloride level and cystic fibrosis. In functional studies, p.R117L was shown to retain normal CFTR maturation/processing, but result in approximately 20% of wild-type CFTR function (Sosnay PR et al. Nat Genet, 2013 Oct;45:1160-7; Van Goor F et al. J. Cyst. Fibros., 2014 Jan;13:29-36). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on available evidence to date, this variant is unlikely to be causative of classic cystic fibrosis when it occurs in isolation; however, its contribution to the development of a CFTR-related disorder is uncertain. This alteration is thus classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina	RCV001009470	SCV001321895	uncertain significance	CFTR-related disorders	2017-04-27	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Mayo Clinic Laboratories, Mayo Clinic	RCV000078991	SCV001714240	uncertain significance	not provided	2021-12-16	criteria provided, single submitter	clinical testing
Pars Genome Lab	RCV000046745	SCV001736787	uncertain significance	Cystic fibrosis	2021-05-18	criteria provided, single submitter	clinical testing
Institute of Reproductive Genetics, University of Münster	RCV001642202	SCV001860327	pathogenic	Obstructive azoospermia	2022-03-16	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV000046745	SCV002507376	uncertain significance	Cystic fibrosis	2019-08-14	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000078991	SCV003831649	uncertain significance	not provided	2023-07-31	criteria provided, single submitter	clinical testing
Eurofins-Biomnis	RCV000046745	SCV003935034	likely pathogenic	Cystic fibrosis	2022-12-01	criteria provided, single submitter	clinical testing
OMIM	RCV000007650	SCV000027851	risk factor	Pancreatitis, idiopathic, susceptibility to	2001-01-01	no assertion criteria provided	literature only
OMIM	RCV000007651	SCV000053490	risk factor	Hypertrypsinemia, neonatal, susceptibility to	2001-01-01	no assertion criteria provided	literature only
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	RCV000583195	SCV000692328	uncertain significance	Pancreatitis	2015-09-15	no assertion criteria provided	clinical testing
MAGI's Lab - Research, MAGI Group	RCV001327946	SCV001432724	uncertain significance	Infertility disorder		no assertion criteria provided	provider interpretation
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000078991	SCV001744100	uncertain significance	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000078991	SCV001928674	uncertain significance	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000078991	SCV001951969	uncertain significance	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000078991	SCV001968505	uncertain significance	not provided		no assertion criteria provided	clinical testing
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals	RCV001009470	SCV002029172	uncertain significance	CFTR-related disorders	2021-10-29	no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV001009470	SCV002507462	likely pathogenic	CFTR-related disorders	2019-08-14	no assertion criteria provided	clinical testing