chr7-117611641-C-T
Variant names:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3_ModeratePP5
The NM_000492.4(CFTR):c.3200C>T(p.Ala1067Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,613,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000077 ( 0 hom. )
Consequence
CFTR
NM_000492.4 missense
NM_000492.4 missense
Scores
14
4
1
Clinical Significance
Conservation
PhyloP100: 7.86
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 Likely_pathogenic. Variant got 7 ACMG points.
PM1
In a helix (size 6) in uniprot entity CFTR_HUMAN there are 6 pathogenic changes around while only 0 benign (100%) in NM_000492.4
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.923
PP5
Variant 7-117611641-C-T is Pathogenic according to our data. Variant chr7-117611641-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 53683.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=6, Pathogenic=1, Likely_pathogenic=4}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFTR | NM_000492.4 | c.3200C>T | p.Ala1067Val | missense_variant | Exon 20 of 27 | ENST00000003084.11 | NP_000483.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152044Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250938Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135618
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:6Uncertain:6
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Cystic fibrosis Pathogenic:2Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Nov 13, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 13, 2024 | The p.A1067V variant (also known as c.3200C>T), located in coding exon 20 of the CFTR gene, results from a C to T substitution at nucleotide position 3200. The alanine at codon 1067 is replaced by valine, an amino acid with similar properties. This variant has been detected in conjunction with a pathogenic CFTR mutation in individuals with congenital bilateral absence of the vas deferens (CBAVD), with no or few other signs of cystic fibrosis; however, the phase of the alterations (cis or trans) was not reported (De Braekeleer M et al. Mol. Hum. Reprod.,1996 Sep;2:669-77; Jézéquel P et al. Mol Hum Reprod, 2000 Dec;6:1063-7). Based on internal structural analysis, this variant is more destabilizing than known pathogenic variants within the domain (Jin MS et al. Nature, 2012 Oct;490:566-9). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 15, 2024 | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1067 of the CFTR protein (p.Ala1067Val). This variant is present in population databases (rs1800114, gnomAD 0.003%). This missense change has been observed in individuals with congenital bilateral absence of the vas deferens and cystic fibrosis (PMID: 7539342, 7689902, 8556303; Invitae). ClinVar contains an entry for this variant (Variation ID: 53683). 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%. This variant disrupts the p.Ala1067 amino acid residue in CFTR. Other variant(s) that disrupt this residue have been observed in individuals with CFTR-related conditions (PMID: 1284639, 8662892, 8702904, 23891399, 27131402), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Apr 27, 2021 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Jul 02, 2021 | - - |
not provided Pathogenic:1Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 11, 2016 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 18, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 10, 2024 | Observed in individuals with congenital absence of the vas deferens who also harbored additional CFTR variants, but segregation data and additional clinical information was not included (PMID: 9239681, 7539342, 8556303, Woods, 2013); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24419263, 7689902, 7539342, 25087612, 1284534, Woods2013[Article], 32734384, 8556303, 11101688, 9239681, 36604502, 34996830, 34782259) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Aug 21, 2024 | PP3, PM2 - |
CFTR-related disorder Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Apr 27, 2021 | - - |
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 | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jun 17, 2024 | The CFTR c.3200C>T; p.Ala1067Val variant (rs1800114; ClinVar Variation ID: 53683) is reported in the literature in individuals affected with congenital absence of vas deferens (CBAVD) or atypical cystic fibrosis, some of whom carry a pathogenic variant on the opposite chromosome (De Braekeleer 1996, Jezequel 1995, Welsh 2014). This variant is only found on three alleles in the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.936). Additionally, other amino acid substitutions at this codon (Thr, Pro, Asp) have been reported in individuals with CF or CFTR-related disorders (Ferec 1992, see link to CF mutation database). While the p.Ala1067Val variant is not predicted to cause classic cystic fibrosis, it is considered to be likely pathogenic for CFTR-related disorders. References: Link to cystic fibrosis mutation database: http://www.genet.sickkids.on.ca/cftr/Home.html De Braekeleer M and Ferec C. Mutations in the cystic fibrosis gene in men with congenital bilateral absence of the vas deferens. Mol Hum Reprod. 1996 Sep;2(9):669-77. PMID: 9239681. Ferec C et al. Detection of over 98% cystic fibrosis mutations in a Celtic population. Nat Genet. 1992 Jun;1(3):188-91. PMID: 1284639. Jezequel P et al. Structural analysis of CFTR gene in congenital bilateral absence of vas deferens. Clin Chem. 1995 Jun;41(6 Pt 1):833-5. PMID: 7539342. Welsh SK et al. False-negative sweat chloride testing in a child with cystic fibrosis and undiagnosed hypohidrotic ectodermal dysplasia. Clin Pediatr (Phila). 2014 Oct;53(12):1203-5. PMID: 24419263. - |
Congenital bilateral aplasia of vas deferens from CFTR mutation Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 19, 2024 | Variant summary: CFTR c.3200C>T (p.Ala1067Val) results in a non-conservative amino acid change located in the ABC transporter type 1, transmembrane 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 1.2e-05 in 250938 control chromosomes (gnomAD). c.3200C>T has been reported in the literature in the compound heterozygous state in individuals affected with Congenital Bilateral Absence Of The Vas Deferens (e.g. Jezequel_1995, DeBraekeleer_1996, Woods_2013, Qu_2023). These data indicate that the variant is likely to be associated with disease. It was also reported as a non-informative genotype in a child with features of atypical CF and hypohydrotic ectodermal dysplasia (Welsh_2014). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 8556303, 9239681, 7539342, 11101688, 36604502, 25735457, 1284534, 24419263). ClinVar contains an entry for this variant (Variation ID: 53683). Based on the evidence outlined above, the variant was classified as likely pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
D;.;.;D;.
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H;.;.;.;.
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;.;.;D;.
REVEL
Pathogenic
Sift
Uncertain
D;.;.;D;.
Sift4G
Pathogenic
D;.;.;D;.
Polyphen
D;.;.;.;.
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at