Submissions for variant NM_000492.4(CFTR):c.221G>A (p.Arg74Gln)

gnomAD frequency: 0.00022  dbSNP: rs142540482

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000046556	SCV000074569	uncertain significance	Cystic fibrosis	2022-10-04	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 74 of the CFTR protein (p.Arg74Gln). This variant is present in population databases (rs142540482, gnomAD 0.05%). This missense change has been observed in individual(s) with chronic pancreatitis (PMID: 17003641, 21520337, 22427236, 25033378). ClinVar contains an entry for this variant (Variation ID: 53456). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CFTR protein function. Experimental studies have shown that this missense change affects CFTR function (PMID: 31561038). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Eurofins Ntd Llc (ga)	RCV000589418	SCV000228894	uncertain significance	not provided	2017-07-19	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000589418	SCV000602983	uncertain significance	not provided	2022-04-26	criteria provided, single submitter	clinical testing	The CFTR c.221G>A; p.Arg74Gln variant (rs142540482) has been reported in multiple pancreatitis patients (Keiles 2006, Masson 2013, Rosendahl 2013, LaRusch 2014) but did not show significant enrichment in patients compared to unaffected individuals (Rosendahl 2013, LaRusch 2014). Functional studies indicate that the variant protein has a defect in bicarbonate transport, but has no impact on chloride transport activity (LaRusch 2014). This variant is reported in ClinVar (Variation ID: 53456) and is found in the non-Finnish European population with an overall allele frequency of 0.05% (64/128878 alleles) in the Genome Aggregation Database. The arginine at residue 74 is moderately conserved, and computational algorithms are uncertain whether this variant is neutral or deleterious (REVEL: 0.483). Due to the limited and conflicting information regarding this variant, its clinical significance cannot be determined with certainty. References: Keiles S et al. Identification of CFTR, PRSS1, and SPINK1 mutations in 381 patients with pancreatitis. Pancreas. 2006 33(3):221-7. PMID: 17003641 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. 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. Rosendahl J et al. CFTR, SPINK1, CTRC and PRSS1 variants in chronic pancreatitis: is the role of mutated CFTR overestimated? 2013 Gut. 62(4):582-92. PMID: 22427236.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000177074	SCV000696890	uncertain significance	not specified	2023-04-27	criteria provided, single submitter	clinical testing	Variant summary: CFTR c.221G>A (p.Arg74Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. One publication (Ramalho_2015) and 2/4 computational tools predict that the variant creates a cryptic 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00026 in 254510 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Chronic Pancreatitis Risk (0.00026 vs 0.0063), allowing no conclusion about variant significance. The variant was reported in one patient with a CFTR-related disorder (unspecified phenotype) however, this patient also carried a pathogenic CFTR variant (c.3846G>A, p.W1282X) in cis, supporting a benign role for the variant of interest in this case (Trujillano_2013). On the other hand, multiple publications cite the variant in individuals with pancreatitis (e.g. Keiles_2006, Steiner_2011, Rosendahl_2012, Masson_2013, LaRusch_2014). In several patients, the variant was reported along with p.R297Q (phase not specified), and this co-occurring variant (i.e. c.890G>A, p.Arg297Gln), was also reported in several patients with idiopathic pancreatitis. Additionally, the variant was found to be associated with pancreatitis in a case control study when patients also have the SPINK1 pathogenic mutation p.N34S (LaRusch_2014). This study also reported experimental evidence that the c.221G>A, p.Arg74Gln variant results in significantly reduced bicarbonate channel function (LaRusch_2014). Similarly, another functional study has reported that the variant impairs the association of CFTR with WNK1, reducing WNK1-mediated regulation of HCO3- channel activity (Kim_2019). Authors of the former study (LaRusch_2014) concluded that variants that impair bicarbonate permeation may increase the risk for pancreatitis, but not for cystic fibrosis. In contrast, a recent meta-analysis of CFTR variants characterized by a selective bicarbonate conductance defect did not find a significant association of p.Arg74Gln with chronic pancreatitis (Berke_2022). The following publications have been ascertained in the context of this evaluation (PMID: 36264955, 17003641, 34973142, 31561038, 25033378, 23951356, 29859674, 34782259, 22427236, 21520337, 23687349). Eleven submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and classfied the variant as either VUS (n=10) or likely benign (n=1). Based on the evidence outlined above, the variant was classified as VUS.
Counsyl	RCV000046556	SCV000794964	uncertain significance	Cystic fibrosis	2017-10-24	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000046556	SCV001175594	uncertain significance	Cystic fibrosis	2022-09-08	criteria provided, single submitter	clinical testing	The p.R74Q variant (also known as c.221G>A), located in coding exon 3 of the CFTR gene, results from a G to A substitution at nucleotide position 221. The arginine at codon 74 is replaced by glutamine, an amino acid with highly similar properties. This variant was reported in an individual with idiopathic chronic pancreatitis who was negative for mutations in the PRSS1 gene (Rosendahl J et al. Pancreatology, 2010 May;10:165-72). Functional studies found that this variant did not affect chloride current density, but significantly reduced bicarbonate permeability and conductance in HEK 293T cells, which may increase the risk of pancreatitis (LaRusch J et al. PLoS Genet., 2014 Jul;10:e1004376; Kim Y et al. Cell Mol Gastroenterol Hepatol, 2020 Sep;9:79-103). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on available evidence, this variant is unlikely to be causative of classic CF, however its clinical contribution to the development of a CFTR-related disorder is uncertain.
Illumina Laboratory Services, Illumina	RCV001161752	SCV001323653	likely benign	CFTR-related disorder	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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Mayo Clinic Laboratories, Mayo Clinic	RCV000589418	SCV001714826	uncertain significance	not provided	2019-05-07	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000046556	SCV001821986	uncertain significance	Cystic fibrosis	2021-07-22	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV000046556	SCV002574022	uncertain significance	Cystic fibrosis	2022-09-05	criteria provided, single submitter	curation	This variant was identified in 1 patient with a clinically confirmed diagnosis of cystic fibrosis. The variant was classified in the context of a project re-classifying variants in the German Cystic Fibrosis Registry (Muko.e.V.). Link: https://www.muko.info/angebote/qualitaetsmanagement/register/cf-einrichtungen/mukoweb. Criteria applied: PS3_SUP, PM3, PM5, BP2, BP4
Johns Hopkins Genomics, Johns Hopkins University	RCV000046556	SCV003839069	uncertain significance	Cystic fibrosis	2023-02-13	criteria provided, single submitter	clinical testing	Previously reported CFTR variant that has been identified in individuals with pancreatitis and has an entry in ClinVar (Variation ID: 53456). This CFTR variant (rs142540482) is rare (<0.1%) in a large population dataset (gnomADv2.1.1: 72/282380 total alleles; 0.0255%; no homozygotes). Functional studies have shown that this variant has a normal chloride current, but impaired conductance of and permeability to bicarbonate. The latter has been be associated with pancreatitis risk. The clinical significance of this variant is uncertain at this time.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000589418	SCV004221671	uncertain significance	not provided	2023-08-21	criteria provided, single submitter	clinical testing	The CFTR c.221G>A (p.Arg74Gln) variant has been reported in the published literature in individuals affected with congenital absence of the vas deferens (PMID: 31845523 (2020), 21520337 (2011)), and pancreatitis (PMID: 17003641 (2006), 20460947 (2010), 21520337 (2011), 22427236 (2013)). Published functional studies show normal but reduced bicarbonate permeability and conductance (PMID: 25033378 (2014), PMID: 31561038 (2020)). The frequency of this variant in the general population, 0.00083 (42/50662 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 conflicting predictions that this variant is deleterious or benign. Based on the available information, we are unable to determine the clinical significance of this variant.
Natera, Inc.	RCV000046556	SCV001453944	uncertain significance	Cystic fibrosis	2018-05-25	no assertion criteria provided	clinical testing