ClinVar Genomic variation as it relates to human health

The p.T1246I pathogenic mutation (also known as c.3737C>T), located in coding exon 23 of the CFTR gene, results from a C to T substitution at nucleotide position 3737. The threonine at codon 1246 is replaced by isoleucine, an amino acid with similar properties. This alteration has been reported as compound heterozygous with another CFTR alteration in several individuals with cystic fibrosis or CFTR-related disorders (Claustres M et al. Hum. Mutat., 2000;16:143-56; Goubau C et al. Thorax, 2009 Aug;64:683-91; Sermet-Gaudelus I et al. Am. J. Respir. Crit. Care Med., 2010 Oct;182:929-36; Masica DL et al. Hum. Mol. Genet., 2015 Apr;24:1908-17). This position has been shown to be important in binding ATP for chloride channel gating, however, the T1246I alteration was not specifically evaluated (Vergani P et al. Nature, 2005 Feb;433:876-80). This variant has been reported in multiple individuals with an elevated sweat chloride level in The Clinical and Functional TRanslation of CFTR (CFTR2) database (available at http://cftr2.org. Accessed 03/29/2022). In CFBE cells, this variant showed reduced CFTR function compared to wild type (Raraigh KS et al. Am. J. Hum. Genet., 2018 06;102:1062-1077; Han ST et al. JCI Insight, 2018 Jul;3(14):pii 121159). The p.T1246I alteration has been reported as a variant of varying clinical consequences (VVCC) (Sosnay PR et al. Pediatr. Clin. North Am., 2016 08;63:585-98; Raraigh KS et al. Am. J. Hum. Genet., 2018 06;102:1062-1077). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

CFTR variant associated with varying clinical consequence. See www.CFTR2.org for phenotype information.

The CFTR c.3737C>T; p.Thr1246Ile variant (rs397508600) is reported in the literature in the compound heterozygous state with a different pathogenic variant in individuals affected with cystic fibrosis, a CFTR-related disorder, or borderline sweat chloride levels with no other significant symptoms (Claustres 2000, El-Seedy 2012, Goubau 2009, Masica 2015, Sermet-Gaudelus 2010, Sosnay 2017). This variant is reported in ClinVar (Variation ID: 53799), and is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. The threonine at codon 1246 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. In vitro functional analyses of the variant protein demonstrate 13% of wild-type function, consistent with an intermediate effect (Raraigh 2018). Based on available information, this variant is considered to be likely pathogenic with variable clinical consequences. References: Claustres M et al. Spectrum of CFTR mutations in cystic fibrosis and in congenital absence of the vas deferens in France. Hum Mutat. 2000;16(2):143-156. El-Seedy A et al. CFTR mutation combinations producing frequent complex alleles with different clinical and functional outcomes. Hum Mutat. 2012;33(11):1557-1565. Goubau C et al. Phenotypic characterisation of patients with intermediate sweat chloride values: towards validation of the European diagnostic algorithm for cystic fibrosis. Thorax. 2009;64(8):683-691. Masica DL et al. Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Hum Mol Genet. 2015;24(7):1908-1917. Raraigh KS et al. Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity. Am J Hum Genet. 2018;102(6):1062-1077. Sermet-Gaudelus I et al. Clinical phenotype and genotype of children with borderline sweat test and abnormal nasal epithelial chloride transport. Am J Respir Crit Care Med. 2010;182(7):929-936. Sosnay PR et al. Diagnosis of Cystic Fibrosis in Nonscreened Populations. J Pediatr. 2017;181S:S52-S57.e2. References: Claustres M et al. Spectrum of CFTR mutations in cystic fibrosis and in congenital absence of the vas deferens in France. Hum Mutat. 2000;16(2):143-156. El-Seedy A et al. CFTR mutation combinations producing frequent complex alleles with different clinical and functional outcomes. Hum Mutat. 2012;33(11):1557-1565. Goubau C et al. Phenotypic characterisation of patients with intermediate sweat chloride values: towards validation of the European diagnostic algorithm for cystic fibrosis. Thorax. 2009;64(8):683-691. Masica DL et al. Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Hum Mol Genet. 2015;24(7):1908-1917. Raraigh KS et al. Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity. Am J Hum Genet. 2018;102(6):1062-1077. Sermet-Gaudelus I et al. Clinical phenotype and genotype of children with borderline sweat test and abnormal nasal epithelial chloride transport. Am J Respir Crit Care Med. 2010;182(7):929-936. Sosnay PR, White TB, Farrell PM, et al. Diagnosis of Cystic Fibrosis in Nonscreened Populations. J Pediatr. 2017;181S:S52-S57.e2.

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, PM2_SUP, PM3_STR, PP3

Variant summary: CFTR c.3737C>T (p.Thr1246Ile) results in a non-conservative amino acid change located in the ABC transporter-like, ATP-binding (IPR003439) and AAA+ ATPase (IPR003593) domains of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 250992 control chromosomes (gnomAD). c.3737C>T has been reported in the literature as a compound heterozygous genotype (mostly in trans with the known pathogenic variant p.Phe508del) in multiple individuals affected with Non-Classic Cystic Fibrosis related phenotypes and has been linked to varying clinical consequences; sweat chloride values were reported to be in the intermediate range for at least some of these individuals (example: Claustres_2000, Goubau_2009, El-Seedy_2012, Sosnay_2017_McCague_2019). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 10%-<30% of normal CFTR activity (Han_2018, Raraigh_2018). Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified it as VUS (n=2), likely pathogenic (n=2) and pathogenic (n=3). Based on the evidence outlined above, the variant was classified as pathogenic, with varying clinical consequences.

This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 1246 of the CFTR protein (p.Thr1246Ile). This variant is present in population databases (rs397508600, gnomAD 0.0009%). This missense change has been observed in individuals with cystic fibrosis, and intermediate sweat chloride results (PMID: 10923036, 19318346, 20538955, 22678879, 28129813). ClinVar contains an entry for this variant (Variation ID: 53799). 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 expected to disrupt CFTR protein function. Experimental studies have shown that this missense change affects CFTR function (PMID: 29805046, 30046002). For these reasons, this variant has been classified as Pathogenic.

The CFTR c.3737C>T variant is predicted to result in the amino acid substitution p.Thr1246Ile. This variant, along with a second CFTR variant, has been reported in individuals with cystic fibrosis (CF) and cystic fibrosis-related disorders (CF-RD), including congenital bilateral absence of the vas deferens (Table 4, Claustres et al. 2000. PubMed ID: 10923036; Table 1, El-Seedy et al. 2012. PubMed ID: 22678879; Sosnay et al. 2017. PubMed ID: 28129813; CFTR-France database, https://cftr.iurc.montp.inserm.fr/cgi-bin/affiche.cgi?variant=c.3737C%3ET). This variant has also been reported in in the CFTR2 Database in more than 20 patients as a variant of varying clinical consequence and has been reported in the heterozygous state in a study of individuals with COPD or asthma (Supplementary Table 1, Saferali et al. 2022. PubMed ID: 34996830; https://cftr2.org/mutation/general/T1246I/). In vitro experimental studies suggest this variant reduces CFTR function to 10%–20% compared to control (Raraigh et al. 2018. PubMed ID: 29805046; Han et al. 2018. PubMed ID: 30046002). An alternate nucleotide substitution affecting the same amino acid (p.Thr1246Ala), has been reported in an individual with male infertility (Table 2, Li et al. 2022. PubMed ID: 34931337). This variant is reported in 0.00088% of alleles in individuals of European (non-Finnish) descent in gnomAD. Taken together, the c.3737C>T (p.Thr1246Ile) variant is interpreted as likely pathogenic.