ClinVar Genomic variation as it relates to human health

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.

Variant summary: The c.1646G>A variant affects a conserved nucleotide, resulting in amino acid change from Ser to Asn. 4/5 in-silico tools predict this variant to be damaging. This variant is found in 13/120694 control chromosomes at a frequency of 0.0001077, which does not exceed maximal expected frequency of a pathogenic allele (0.0129603). This variant is a well-known pathogenic variant and has been reported in numerous CF patients. Variants affecting same amino acid, i.e. p.Ser549Arg, p.Ser549Ile, have been classified as pathogenic, suggesting Ser549 is critical for CFTR function. In addition, multiple clinical laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant was classified as pathogenic.

NM_000492.3(CFTR):c.1646G>A(S549N) is classified as pathogenic in the context of cystic fibrosis and is associated with the classic form of the disease. Sources cited for classification include the following: PMID 1695717, 18456578, and 23974870. Classification of NM_000492.3(CFTR):c.1646G>A(S549N) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

The CFTR c.1646G>A; p.Ser549Asn variant (rs121908755) is reported in the literature as a common variant in individuals affected with cystic fibrosis, and is associated with pancreatic insufficiency (Castellani 2008, Cutting 1990, Masica 2015, Sharma 2015, Sosnay 2013). This variant is also reported in individuals affected with CFTR-related disorders when found with a pathogenic-mild variant on the opposite chromosome (Masson 2013, Ooi 2012, Sharma 2014). This variant is reported in ClinVar (Variation ID: 7116), and is found in the general population with an overall allele frequency of 0.0085% (24/282312 alleles) in the Genome Aggregation Database. The serine at codon 549 is highly conserved and is located in the ATP binding site, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. In vitro functional analyses demonstrate defects in channel gating and function (Sharma 2015, Yu 2012). Additionally, other variants at this codon (c.1645A>C; p.Ser549Arg, c.1647T>G; p.Ser549Arg) have been reported in individuals with cystic fibrosis and are considered pathogenic (Castellani 2008, Masica 2015, Sosnay 2013). Based on available information, the p.Ser549Asn variant is considered to be pathogenic. References: Castellani C et al. Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros. 2008 May;7(3):179-96. Cutting GR et al. A cluster of cystic fibrosis mutations in the first nucleotide-binding fold of the cystic fibrosis conductance regulator protein. Nature. 1990 Jul 26;346(6282):366-9. Masica DL et al. Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Hum Mol Genet. 2015 Apr 1;24(7):1908-17. 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. Ooi CY and Durie PR. Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in pancreatitis. J Cyst Fibros. 2012 Sep;11(5):355-62. Sharma H et al. Heterogeneous spectrum of mutations in CFTR gene from Indian patients with congenital absence of the vas deferens and their association with cystic fibrosis genetic modifiers. Mol Hum Reprod. 2014 Sep;20(9):827-35. Sharma H et al. Function, pharmacological correction and maturation of new Indian CFTR gene mutations. J Cyst Fibros. 2015 Jan;14(1):34-41. Sosnay PR et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet. 2013 Oct;45(10):1160-7. Yu H et al. Ivacaftor potentiation of multiple CFTR channels with gating mutations. J Cyst Fibros. 2012 May;11(3):237-45.

The variant was found in at least one symptomatic individual. The variant predicted to have a damaging effect on the protein. The variant occurs in multiple cases with a lone recessive pathogenic/likely pathogenic variant in the same gene, and several have a phenotype known to be consistent with disease. The variant is damaging to protein function(s) relevant to disease mechanism.

This heterozygous mis-sense variant is identified in a 4 month female with fever, respiratory infection, seizures, and epileptic encephalopathy. This nucleotide change is present in gnomAD database with a low allele frequency 0.0085% [PM2]. Insilico prediction [REVEL=0.91] predicts deleterious nature of this variant [PP3]. This variant is identified in trans [PM3] with a previously reported “Pathogenic” p.Phe508del variant . A clinvar entry for this variant is available. This variant is submitted to clinvar database [Variation ID: 7116] with “Pathogenic” interpretation by multiple submitter [PP5]. Based on the clinical correlation and available evidence, this variant is classified as "Pathogenic".

The CFTR c.1646G>A variant is predicted to result in the amino acid substitution p.Ser549Asn. This variant has previously been reported to be causative for cystic fibrosis (Cutting et al. 1990. PubMed ID: 1695717; Hamosh et al. 1991. PubMed ID: 1721624; Brancolini et al. 1995. PubMed ID: 7544319; Watson et al. 2004. PubMed ID: 15371902; Sosnay et al. 2013. PubMed ID: 23974870; De Boeck et al. 2014. PubMed ID: 24440181; Sharma et al. 2014. PubMed ID: 25042876; Sutanto et al. 2018. PubMed ID: 29360847). This variant was also reported in at least two patients with pancreatitis (Ooi et al. 2012. PubMed ID: 22658665). This variant is reported in 0.039% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-117227854-G-A). This variant is interpreted as pathogenic.

Disease-causing CFTR variant (previously reported for this patient by mass spectrometry genotyping). See www.CFTR2.org for phenotype information.

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

The c.1646G>A (p.Ser549Asn) missense variant in CFTR gene has been reported in individuals affected with cystic fibrosis, and is associated with pancreatic insufficiency (Ooi CY, Durie PR., 2015; Sharma et al., 2015). Experimental studies have shown that this variant causes defective channel gating, resulting in decreased chloride conductance (Sharma et al., 2015). This variant is reported with the allele frequency (0.008%) in the gnomAD and novel in 1000 genome database. This variant has been reported to the ClinVar database as Pathogenic. The amino acid Ser at position 549 is changed to a Asn changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Ser549Asn in CFTR is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 549 of the CFTR protein (p.Ser549Asn). This variant is present in population databases (rs121908755, gnomAD 0.04%). This missense change has been observed in individual(s) with cystic fibrosis or congenital absence of the vas deferens (PMID: 1695717, 1721624, 7544319, 22658665, 23974870, 24440181, 25042876, 29360847). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.1778G>A. ClinVar contains an entry for this variant (Variation ID: 7116). 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 with a positive predictive value of 80%. Experimental studies have shown that this missense change affects CFTR function (PMID: 22293084, 23974870, 25042876). This variant disrupts the p.Ser549 amino acid residue in CFTR. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The p.S549N pathogenic mutation (also known as c.1646G>A), located in coding exon 12 of the CFTR gene, results from a G to A substitution at nucleotide position 1646. The serine at codon 549 is replaced by asparagine, an amino acid with highly similar properties. This mutation was identified in a homozygous individual with an elevated sweat chloride level, growth failure, reduced lung function, and Psuedomonas aeruginosa colonization (Curtis A et al. J. Med. Genet., 1993 Feb;30:164-6). This mutation is associated with elevated sweat chloride levels and pancreatic insufficiency; in addition, a functional study found this mutation resulted in significantly decreased rates of chloride conductance compared to wild type (Sosnay PR et al. Nat Genet. 2013; 45(10):1160-7). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.