Submissions for variant NM_000492.4(CFTR):c.220C>T (p.Arg74Trp)

gnomAD frequency: 0.00350  dbSNP: rs115545701

Total submissions: 20

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PharmGKB	RCV000660770	SCV000783009	drug response	ivacaftor response - Efficacy	2021-03-24	reviewed by expert panel	curation	PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.
Eurofins Ntd Llc (ga)	RCV000224532	SCV000228891	likely pathogenic	not provided	2018-08-03	criteria provided, single submitter	clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV000224532	SCV000281538	likely pathogenic	not provided	2015-03-23	criteria provided, single submitter	clinical testing
Invitae	RCV000177071	SCV000562311	benign	Cystic fibrosis	2024-02-01	criteria provided, single submitter	clinical testing
GeneDx	RCV000479747	SCV000568547	uncertain significance	not specified	2016-06-10	criteria provided, single submitter	clinical testing	The R74W variant in the CFTR gene has been reported previously as heterozygous in one individual with CF; no other variants in the CFTR gene were identified in this individual (Claustres et al., 1993). Expression studies in FRT cells showed that D1270N transfected cells displayed decreased chloride transport activity compared to wild type cells (Van Goor et al., 2014). However, an earlier functional study in HeLa cells showed that D1270N transfected cells displayed chloride transport kinetics similar to wild type cells (Fanen et al., 1999). The R74W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position where amino acids with similar properties to Arginine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret R74W as a variant of uncertain significance.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000224532	SCV000601070	likely pathogenic	not provided	2023-03-30	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000224532	SCV000602984	uncertain significance	not provided	2023-10-27	criteria provided, single submitter	clinical testing	The CFTR c.220C>T; p.Arg74Trp variant (rs115545701) is reported in the medical literature as part of a complex allele with other variants, c.601G>A and c.3808G>A, on the same chromosome in individuals diagnosed with pancreatitis, infertility and/or congenital absence of vas deferens, often in trans with another pathogenic CFTR variant (Bareil 2007, Brugnon 2008, Claustres 2004, Gallati 2009, Lucarelli 2015, Masson 2013, Picci 2010, Steiner 2011). However, the p.Arg74Trp variant has not been described alone in the medical literature in individuals who are clinically affected with a CFTR-related disorder. Alone this variant contains an entry in ClinVar (Variation ID: 196277) and is observed in the general population databases at a frequency of 0.17% (485/282362 alleles, 3 homozygotes) in the Genome Aggregation database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.476). Functional analyses suggest this variant has modestly decreased chloride channel activity (44% of wildtype), but it is unclear if this difference is clinically significant (Van Goor 2014). Considering available information, the clinical significance of the p.Arg74Trp variant when discovered alone is uncertain at this time. References: Bareil C et al. Comprehensive and rapid genotyping of mutations and haplotypes in congenital bilateral absence of the vas deferens and other cystic fibrosis transmembrane conductance regulator-related disorders. J Mol Diagn. 2007 Nov;9(5):582-8. PMID: 17975025. Brugnon F et al. Outcome of intracytoplasmic sperm injection for a couple in which the man is carrier of CFTR p.[R74W;V201M;D1270N] and p.P841R mutations and his spouse a heterozygous carrier of p.F508del mutation of the cystic fibrosis transmembrane conductance regulator gene. Fertil Steril. 2008 Nov;90(5):2004.e23-6. PMID: 18703181. Claustres M et al. Are p.I148T, p.R74W and p.D1270N cystic fibrosis causing mutations? BMC Med Genet. 2004 Aug 2;5:19. PMID: 15287992. Gallati S et al. Cystic fibrosis transmembrane conductance regulator mutations in azoospermic and oligospermic men and their partners. Reprod Biomed Online. 2009 Nov;19(5):685-94. PMID: 20021716. Lucarelli M et al. A Genotypic-Oriented View of CFTR Genetics Highlights Specific Mutational Patterns Underlying Clinical Macrocategories of Cystic Fibrosis. Mol Med. 2015 Apr 21;21:257-75. PMID: 25910067. 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 Aug 8;8(8):e73522. PMID: 23951356. Picci L et al. A 10-year large-scale cystic fibrosis carrier screening in the Italian population. J Cyst Fibros. 2010 Jan;9(1):29-35. PMID: 19897426. Steiner B et al. Common CFTR haplotypes and susceptibility to chronic pancreatitis and congenital bilateral absence of the vas deferens. Hum Mutat. 2011 Aug;32(8):912-20. PMID: 21520337. 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 Jan;13(1):29-36. PMID: 23891399.
Counsyl	RCV000177071	SCV000800736	uncertain significance	Cystic fibrosis	2017-11-25	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000177071	SCV000916174	uncertain significance	Cystic fibrosis	2016-07-27	criteria provided, single submitter	clinical testing	The CFTR c.220C>T (p.Arg74Trp) variant is reported in four studies with clinical information. Claustres et al. (1993) report the variant in a compound heterozygous state in an individual with cystic fibrosis (CF). In this case, the p.Arg74Trp variant is found alone. Luzardo et al. (2002) report one patient with CF carrying the p.Arg74Trp variant as part of the complex allele p.[R74W+D1270N] in a heterozygous state. Claustres et al. (2004) report three patients with congenital absence of the vas deferens (CBAVD) carrying the complex allele p.[R74W+p.D1270N+p.V201M]. They also report two non-CF or asymptomatic patients carrying the p.[R74W+D1270N] complex allele in a heterozygous state and one CF patient with the p.[R74W+D1270N] complex allele in a compound heterozygous state with another missense variant. de Prada Merino et al. (2010) report the p.Arg74Trp variant in an individual with CF in a compound heterozygous state as part of the complex allele p.[R74W+R1070W+D1270N]. Control data are unavailable for this variant, which is reported at a frequency of 0.03540 in the Mandinka in the Gambia population of the 1000 Genomes Project. The evidence for this variant alone is limited. The p.Arg74Trp variant is therefore classified as a variant of unknown significance but suspicious for pathogenicity for CFTR-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000479747	SCV000967179	likely benign	not specified	2018-07-06	criteria provided, single submitter	clinical testing	The p.Arg74Trp variant in CFTR has been reported as a complex allele (p.[Arg74Tr p;Asp1270Asn] or p.[Arg74Trp;Val201Met;Asp1270Asn]) in several individuals with CFTR-related conditions (Aguiano 1992, Casals 1995, Fanen 1999, Padoa 1999, Ravn ik-Glavac 2000, Luzardo 2002, Girodon 2002, Masson 2013, Sosnay 2013, Terlizzi 2 017, Behar 2017, Claustres 20004, Brugnon 2008, de Prada Merino 2010, Steiner 20 11). However, it has also been reported in 1 unaffected child who carried the p. [Arg74Trp;Asp1270Asn] complex allele in trans with a known pathogenic variant (T erlizzi 2017) and in unaffected twins who carried the p.[Arg74Trp;Val201Met;Asp1 270Asn] complex allele in trans with p.Phe508del (Terlizzi 2017, Brugnon 2008). In addition, the p.Arg74Trp variant has been identified in 1.3% (311/24024) of A frican chromosomes, including 3 homozygotes, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org). An in vitro functional study suggest ed that the p.Arg74Trp variant did not impact protein function (Fanen 1999). Due to its high frequency in GnomAD and observation in unaffecteds, the p.Arg74Trp variant is classified as likely benign. ACMG/AMP Criteria applied: BS1.
Mendelics	RCV000177071	SCV001137467	likely benign	Cystic fibrosis	2019-05-28	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000177071	SCV001175554	uncertain significance	Cystic fibrosis	2023-01-17	criteria provided, single submitter	clinical testing	The p.R74W variant (also known as c.220C>T) is located in coding exon 3 of the CFTR gene. This variant results from a C to T substitution at nucleotide position 220. The arginine at codon 74 is replaced by tryptophan, an amino acid with dissimilar properties. This variant was initially described as disease-causing in isolation (Claustres M et al.Hum Mol Genet. 1993;2(8):1209-1213), but it was later described as part of a complex allele p.[R74W; D1270N] in two individuals unaffected with cystic fibrosis, one of whom was confirmed to have another mutation in trans (Claustres M et al. BMC Med Genet.2004;5:19). This variant is also part of the complex allele p.[R74W; V201M; D1270N] (de Prada Merino A et al. J. Cyst. Fibros. 2010; 9(6):447-9). This complex allele has been identified in the homozygous state and in trans with a pathogenic CFTR mutation in individuals with congenital bilateral absence of the vas deferens (Steiner B et al. Hum. Mutat. 2011; 32(8):912-20). Furthermore, one functional study found that the p.R74W variant slightly reduced the amount of normal CFTR protein, but the rate of cAMP-responsive anion conductance remained the same as wild type (Fanen P et al. FEBS Lett.1999;452(3):371-374). As such, p.R74W was postulated to be a variant that has no deleterious effect alone, but it may enhance the effect of another alteration when found in cis. Based on protein sequence alignment, this amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Johns Hopkins Genomics, Johns Hopkins University	RCV000177071	SCV001430643	likely pathogenic	Cystic fibrosis	2020-06-11	criteria provided, single submitter	clinical testing	CFTR variant associated with varying clinical consequence. See www.CFTR2.org for phenotype information.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000479747	SCV001432075	uncertain significance	not specified	2023-01-30	criteria provided, single submitter	clinical testing	Variant summary: CFTR c.220C>T (p.Arg74Trp) results in a non-conservative amino acid change in 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 0.0042 in 153760 control chromosomes (gnomAD v3 genomes dataset and publication data), predominantly at a frequency of 0.013 within the African or African-American subpopulation, including 6 homozygotes in the gnomAD database (v3 genomes dataset). This frequency is close to the estimated maximal expected allele frequency for a pathogenic variant in CFTR causing Cystic Fibrosis phenotype (0.013). However, the c.220C>T (p.Arg74Trp) variant is frequently reported in complex (i.e. in cis) with ether the c.3808G>A (p.Asp1270Asn) and/or c.601G>A (p.Val201Met) variant. The first two variants (i.e. R74W and D1270N) were individually found in control databases at very similar frequencies and allele counts in the African subpopulation, and variant co-occurrence (phasing) information in gnomAD indicates that these two variants are likely in cooccurrence (i.e. on the same haplotype) within the African, Latino/Admixed American and European (non-Finnish) subpopulations. Therefore, it is very likely that the majority of the gnomAD population carried the [R74W;D1270N] complex allele. Independent studies have shown that the R74W variant protein matures fully with complete processing (Fanen_1999), but in vitro assays have also shown a minor impact on splicing (i.e. an increase in exon 3 skipping; Aissat_2013), and a mild impairment on chloride channel function (Van Goor_2013). An extensive amount of published case studies report this variant as part of different complex alleles, e.g. p.[R74W;D1270N], p.[R74W;V201M;D1270N], p.[TG12T5;R74W], in affected individuals mostly associated with CFTR-RD and particularly CBAVD. However, these complex alleles have been also found in trans with a severe CF-causing variant in asymptomatic (i.e. non-CF) individuals (Claustres_2017, Verlingue_1993), thus they may not be sufficient to cause a classic CF disease phenotype. In conclusion, there is no sufficient evidence to suggest that the R74W variant in isolation, when combined with a deleterious variant in trans, is pathogenic. The variant was classified as indeterminate by Sosnay et al (2013), while the CFTR2 database lists the isolated variant as variant of varying clinical consequence. Multiple other submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, and classified the variant conflicting assessments as pathogenic/likely pathogenic (n=6), VUS (n=7), likely benign/benign (n=4). Based on the evidence outlined above, the variant was classified as uncertain significance.
Baylor Genetics	RCV000177071	SCV001482566	pathogenic	Cystic fibrosis	2020-06-20	criteria provided, single submitter	clinical testing	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Mayo Clinic Laboratories, Mayo Clinic	RCV000224532	SCV001714825	uncertain significance	not provided	2023-05-23	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000177071	SCV001737208	uncertain significance	Cystic fibrosis	2021-05-18	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000224532	SCV001962088	uncertain significance	not provided	2021-07-01	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV002256094	SCV002529687	likely benign	Hereditary pancreatitis	2020-12-21	criteria provided, single submitter	curation
PreventionGenetics, part of Exact Sciences	RCV003416087	SCV004117552	uncertain significance	CFTR-related condition	2023-12-08	criteria provided, single submitter	clinical testing	The CFTR c.220C>T variant is predicted to result in the amino acid substitution p.Arg74Trp. This variant has been reported in the heterozygous state, in the absence of a second variant, in an individual with cystic fibrosis (Claustres et al. 1993. PubMed ID: 7691344) and in a patient with congenital bilateral absence of the vas deferens (Chamayou et al. 2020. PubMed ID: 32357917). The p.Arg74Trp variant resulted in minimal disruption to CFTR processing in HeLa and FRT cells, suggesting normal CFTR maturation (Fanen et al. 1999. PubMed ID: 10386624; Sosnay et al 2013. PubMed ID: 23974870; Van Goor et al. 2014. PubMed ID: 23891399). In FRT cells, the p.Arg74Trp variant retained nearly half of wild-type CFTR chloride channel transport function, which was restored to wild-type levels with ivacaftor, suggesting a mild defect in channel conductance (Sosnay et al 2013. PubMed ID: 23974870; Van Goor et al. 2014. PubMed ID: 23891399). However, in HeLa cells, the p.Arg74Trp variant did not affect cAMP-responsive anion conductance of CFTR (Fanen et al. 1999. PubMed ID: 10386624). The p.Arg74Trp variant is documented in 40 patients in the CFTR2 database with an average sweat chloride concentration of 61 mEq/L, compared to an average of 96 mEq/L for all patients in CFTR2 with two CF-causing variants (cftr2.org). This variant is reported in up to ~1.3% of alleles in individuals of African descent in gnomAD, including three homozygous individuals of unknown phenotype. In ClinVar, this variant has conflicting interpretations of pathogenicity ranging from benign to pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/196277). In summary, due to conflicting genetic and functional evidence, the clinical significance of the p.Arg74Trp variant is uncertain. Of note, the p.Arg74Trp and p.Asp1270Asn variants have been reported in linkage (on the same allele) and are collectively referred to as p.[Arg74Trp;Asp1270Asn]. Variant phasing information in gnomAD indicates that the p.Arg74Trp and p.Asp1270Asn variants likely occur in cis within the African, Latino/Admixed American and European (non-Finnish) subpopulations, but may rarely occur independently of each other. Consistent with this, one study observed that 94% of individuals carrying the p.Asp1270Asn variant also carried the p.Arg74Trp variant (Sugarman et al. 2004. PubMed ID: 15371903). The p.[Arg74Trp; Asp1270Asn] complex allele has been reported in compound heterozygous individuals with CBAVD and obstructive bronchitis (Claustres et al. 2004. PubMed ID: 15287992; Terlizzi et al. 2017. PubMed ID: 27738188; Chamayou et al. 2020. PubMed ID: 32357917), but has also been observed in the compound heterozygous state in asymptomatic individuals (Verlingue et al. 1993. PubMed ID: 7513889; Claustres et al. 2004. PubMed ID: 15287992; Terlizzi et al. 2017. PubMed ID: 27738188). In HeLa cells, the p.[Arg74Trp; Asp1270Asn] variant did not affect CFTR processing but did result in impaired cAMP-responsive anion conductance (Fanen et al. 1999. PubMed ID: 10386624). The authors suggest that both variants together may lead to a synergistic effect to further impair CFTR function than either variant in isolation (Fanen et al. 1999. PubMed ID: 10386624; Claustres et al. 2004. PubMed ID: 15287992). In addition, Sosnay et al. in a comprehensive study of CFTR variants classified these variants as “indeterminate” (Sosnay et al 2013. PubMed ID: 23974870). In ClinVar, the complex allele p.[Arg74Trp; Asp1270Asn] is interpreted as uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/977735). In summary, due to the conflicting genetic and functional evidence, the clinical significance of the complex p.[Arg74Trp; Asp1270Asn] variant is also uncertain.