rs147422190
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP5
The NM_000492.4(CFTR):c.1327G>T(p.Asp443Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000573 in 1,612,974 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00032 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00060 ( 0 hom. )
Consequence
CFTR
NM_000492.4 missense
NM_000492.4 missense
Scores
4
11
3
Clinical Significance
Conservation
PhyloP100: 2.77
Genes affected
CFTR (HGNC:1884): (CF transmembrane conductance regulator) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. The encoded protein functions as a chloride channel, making it unique among members of this protein family, and controls ion and water secretion and absorption in epithelial tissues. Channel activation is mediated by cycles of regulatory domain phosphorylation, ATP-binding by the nucleotide-binding domains, and ATP hydrolysis. Mutations in this gene cause cystic fibrosis, the most common lethal genetic disorder in populations of Northern European descent. The most frequently occurring mutation in cystic fibrosis, DeltaF508, results in impaired folding and trafficking of the encoded protein. Multiple pseudogenes have been identified in the human genome. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM1
In a domain ABC transporter 1 (size 223) in uniprot entity CFTR_HUMAN there are 54 pathogenic changes around while only 9 benign (86%) in NM_000492.4
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 7-117548758-G-T is Pathogenic according to our data. Variant chr7-117548758-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 53229.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=5, Pathogenic=8, Likely_pathogenic=10}. Variant chr7-117548758-G-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CFTR | NM_000492.4 | c.1327G>T | p.Asp443Tyr | missense_variant | 10/27 | ENST00000003084.11 | NP_000483.3 | |
| CFTR-AS1 | NR_149084.1 | n.222-6219C>A | intron_variant |
Ensembl
Frequencies
GnomAD3 genomes 0.000322 AC: 49AN: 152202Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000264 AC: 64AN: 242156Hom.: 0 AF XY: 0.000297 AC XY: 39AN XY: 131380
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GnomAD4 exome AF: 0.000600 AC: 876AN: 1460654Hom.: 0 Cov.: 36 AF XY: 0.000586 AC XY: 426AN XY: 726584
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GnomAD4 genome 0.000322 AC: 49AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74484
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:19Uncertain:5
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Cystic fibrosis Pathogenic:9Uncertain:2
| Pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 443 of the CFTR protein (p.Asp443Tyr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in trans with a pathogenic variant in individuals affected with congenital absence of the vas deferens (CAVD) (PMID: 21520337). Additionally, this variant frequently occurs in cis with the missense variants p.Gly576Ala and p.Arg668Cys. This haplotype has been reported in individuals affected by CFTR-related diseases including CAVD, idiopathic chronic pancreatitis (ICP), chronic sinusitus, and bronchiectasis (PMID: 10922395, 21520337, 22678879, 23951356, 15126740). ClinVar contains an entry for this variant (Variation ID: 53229). 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 protein function (PMID: 22678879). Furthermore, when this variant occurs in combination with p.Gly576Ala and p.Arg668Cys, CFTR chloride channel conductance is decreased. For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | DASA | Mar 05, 2022 | Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 22678879; 29805046) - PS3_supporting.The c.1327G>T;p.(Asp443Tyr) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 53229; PMID: 21520337; PMID: 10922395; PMID: 22678879; PMID: 23951356; PMID: 15126740; PMID: 32512765; PMID: 32172930) - PS4. The variant is located in a mutational hot spot and/or critical and well-established functional domain (ABC_tran) - PM1. The variant is present at low allele frequencies population databases (rs147422190 – gnomAD 0.002595%; ABraOM 0.000854 frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Asp443Tyr) was detected in trans with a pathogenic variant (PMID: 21520337) - PM3. The variant co-segregated with disease in multiple affected family members (PMID: 25133958; 20186691) - PP1. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. The variant was observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern - (PMID: 21520337) - BP2. In summary, the currently available evidence indicates that the variant is pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 25, 2020 | Variant summary: CFTR c.1327G>T (p.Asp443Tyr) results in a non-conservative amino acid change located in the ABC transporter-like domain 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 0.00026 in 242986 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in CFTR causing Classic or Non-Classic Cystic Fibrosis, allowing no conclusion about variant significance. This variant has also been reported to form a haplotype with two other variants, namely, c.1727G>C (p.Gly576Ala) and c.2002C>T (p.Arg668Cys). This complex haplotype c.[1327G>T;1727G>C;2002C>T] (p.[Asp443Tyr;Gly576Ala;Arg668Cys]), has been reported to be pathogenic for CFTR-RD. When ascertained conservatively for its occurrence in isolation, c.1327G>T alone (without the complex haplotype) has been reported in the literature in a compound heterozygous state with other pathogenic CFTR alleles in multiple individuals affected with features of sweat chloride positive classic Cystic Fibrosis, Non-classic Cystic Fibrosis such as CBAVD and settings of infertility (example, Claustres_2000, Steiner_2011, Viville_2000, Morea_2005). However, non-reporting of the other two variants that would constitute a complex allele in these reports cannot be entirely ruled out. Nevertheless, these data indicate that this variant is very likely to be associated with disease. Several publications report experimental evidence evaluating an impact on protein function in isolation as well as part of the complex haplotype. The most pronounced isolated variant effect reports conflicting findings between studies ranging from no effect (El-Seedy_2012) to intermediate levels (Raraigh_2018) of chloride channel function (approximately 50% of WT levels) and a moderate alteration of CFTR maturation and localization (El-Seedy_2012). In one of these studies, the authors concluded that the combination of p.Gly576Ala and p.Arg668Cys affecting chloride channel activity coupled with p.Asp443Tyr effecting protein maturation would account for the pathogenicity of the overall haplotype (El-Seedy_2012). In contrast however, c.1727G>C and c.2002C>T have been reported as non-CF causing in isolation based on a large study evaluating the functional consequences of CFTR variants (Sosnay_2013). Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (Pathogenic, n=2, Likely pathogenic, n=3, and VUS, n=1). Some of these submitters have cited overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant in isolation was classified as pathogenic for CFTR-related disorders. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Mendelics | Nov 05, 2018 | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2024 | The p.D443Y variant (also known as c.1327G>T), located in coding exon 10 of the CFTR gene, results from a G to T substitution at nucleotide position 1327. The aspartic acid at codon 443 is replaced by tyrosine, an amino acid with highly dissimilar properties. This alteration has been described as part of a complex allele (p.[D443Y;G576A;R668C] or p.[D443Y;G576A]) in individuals with CFTR-related disorders, including congenital absence of the vas deferens (CAVD) and chronic pancreatitis; a second alteration was not always detected, nor phase (cis vs. trans) described (Bombieri C et al. J. Cyst. Fibros., 2011 Jun;10 Suppl 2:S86-102; Steiner B et al. Hum. Mutat., 2011 Aug;32:912-20; Masson E et al. PLoS ONE, 2013 Aug;8:e73522). In vitro functional studies showed that this alteration affects protein maturation. In one study, p.D443Y showed decreased chloride channel activity when co-expressed with p.G576A and p.R668C, but not when expressed alone in cultured cells (El-Seedy et al. Hum Mutat. 2012; 33(11);15557-65). In another study, this variant showed decreased chloride channel activity when expressed alone (Raraigh KS et al. Am. J. Hum. Genet. 2018 Jun;102(6):1062-1077). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Johns Hopkins Genomics, Johns Hopkins University | Aug 20, 2020 | CFTR variant associated with varying clinical consequence. See www.CFTR2.org for phenotype information. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Sep 18, 2018 | The CFTR c.1327G>T (p.Asp443Tyr) missense variant has been reported in a compound heterozygous state in five individuals with chronic sinusitis and bronchitis and in a heterozygous state in one proband with congenital uni- or bilateral absence of the vas deferens (de Meeus et al. 1997; Mieusset et al. 2016). The p.Asp443Tyr variant has been reported as part of a complex allele, in cis with c.1727G>C (p.Gly576Ala) and c.2002C>T (p.Arg668Cys) in 57 probands in a compound heterozygous state and in three probands in a heterozygous state (El-Seedy et al. 2012; Abou Alaiwa et al. 2014). Abramowicz et al. (2000) reported the p.[Asp443Tyr;Gly576Ala;Arg668Cys] variant in a compound heterozygous state in a fetus with hyperechoic bowel, a sibling with a history of lower respiratory tract infection and slightly raised sweat chloride, and in an asymptomatic sibling. The p.[Asp443Tyr;Gly576Ala;Arg668Cys] complex allele has been reported in four of 1,423 controls. The p.Asp443Tyr variant is reported at a frequency of 0.000461 in the European (non-Finnish) population of the Genome Aggregation Database. Functional studies indicate that p.[Asp443Tyr;Gly576Ala;Arg668Cys] alters CFTR maturation and chloride conductance but retains some residual function, which is consistent with mild or moderate phenotypes. Based on the evidence, the p.Asp443Tyr variant is classified as likely pathogenic for CFTR-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 02, 2018 | - - |
| Likely pathogenic, criteria provided, single submitter | curation | Institute of Human Genetics, University of Leipzig Medical Center | Sep 05, 2022 | 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_MOD, PM3_STR, PP3 - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Oct 01, 2019 | - - |
not provided Pathogenic:5Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jun 02, 2023 | In the published literature, this variant has been reported as part of a complex allele (PMIDs: 10601093 (1999), 10922395 (2000), 19812525 (2010), 26900683 (2016), and 32773111 (2020)) and observed in CFTR-Related disorders, mostly CBAVD and pancreatitis (PMIDs: 10200050 (1998), 10601093 (1999), 19812525 (2000), 15097853 (2004), 16126774 (2005), 17413420 (2007), 17975025 (2007), 17329263 (2007), 20100616 (2010), 21520337 (2011), 22678879 (2012), 23951356 (2013), 26990548 (2016), and 26946416 (2017)). In vitro functional studies have shown that this variant does not affect chloride channel activity, but it may affect CFTR protein maturation and subcellular localization (PMID: 22678879 (2012)). Another study indicates that this variant is associated with 53.2% of wild type CFTR function that may not be disease-causing (PMID: 29805046 (2018)). The frequency of this variant in the general population, 0.00048 (60/123724 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. - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | CFTR: PM3:Very Strong, PM2 - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jul 06, 2023 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 14, 2012 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 17, 2020 | The CFTR c.1327G>T; p.Asp443Tyr variant (rs147422190), is described in the literature in several individuals with CBAVD who carry a pathogenic severe variant on the opposite allele (de Meeus 1998). This variant is often associated with other variants in cis (G576A, R668C) as a complex allele, and as such is reported to cause a wide range of symptoms including individuals who are asymptomatic even with a pathogenic severe allele on the opposite chromosome, CBAVD, idiopathic pancreatitis, disseminated bronchiectasis, fetal bowel anomaly, and chronic sinus disease (El-Seedy 2012). This variant is classified as a variant of varying clinical consequences in the CFTR2 database (see link), and is reported in ClinVar (Variation ID: 53229). It is found in the general European population with an allele frequency of 0.05% (60/123724 alleles) in the Genome Aggregation Database, but may be a low quality site in this database. The aspartate at codon 443 is moderately conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant may be deleterious. Based on available information, this variant is considered to be mildly pathogenic for CFTR-related disorders. References: CFTR2 database: https://cftr2.org de Meeus A et al. Genetic findings in congenital bilateral aplasia of vas deferens patients and identification of six novel mutatations. Mutations in brief no. 138. Online. Hum Mutat. 1998;11(6):480. El-Seedy A et al. CFTR mutation combinations producing frequent complex alleles with different clinical and functional outcomes. Hum Mutat. 2012 Nov;33(11):1557-65. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | AiLife Diagnostics, AiLife Diagnostics | Jul 09, 2020 | - - |
CFTR-related disorder Pathogenic:2
| Likely pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Oct 01, 2019 | - - |
| Pathogenic, criteria provided, single submitter | curation | CFTR-France | Mar 26, 2018 | - - |
Cystic fibrosis;C0403814:Congenital bilateral aplasia of vas deferens from CFTR mutation Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
Cystic fibrosis;C0238339:Hereditary pancreatitis;C0403814:Congenital bilateral aplasia of vas deferens from CFTR mutation;C2749757:Bronchiectasis with or without elevated sweat chloride 1 Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 05, 2024 | - - |
Bronchiectasis with or without elevated sweat chloride 1 Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 26, 2024 | - - |
not specified Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 05, 2014 | The Asp443Tyr variant in CFTR has been reported in >50 compound heterozygous ind ividuals with varying clinical diagnoses, including congenital bilateral absence of the van deferens (CBAVD), diffuse bronchiectasis, idiopathic pancreatitis, a nd cystic fibrosis (de Meeus 1997, El-Seedy 2012); however most of these individ uals carried one or more CFTR variants in cis with this variant. This variant be en identified in 2/8588 European American and 2/4400 African American chromosome s by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSN P rs147422190). Functional data suggest that the Asp443Tyr variant may alter CFT R protein maturation (El-Seedy 2012), however this in vivo assay may not accurat ely reflect biological function. Computational prediction tools and evolutionary conservation analysis do not provide strong support for or against an impact to the protein. In summary, the clinical significance of the Asp443Tyr variant is uncertain. - |
Hereditary pancreatitis Uncertain:1
| Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Apr 23, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Pathogenic
D;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D
REVEL
Pathogenic
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
P;.
Vest4
MVP
MPC
ClinPred
D
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at