rs193922516
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_000492.4(CFTR):c.3038C>A(p.Pro1013His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,218 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1013L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000492.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFTR | NM_000492.4 | c.3038C>A | p.Pro1013His | missense_variant | 19/27 | ENST00000003084.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFTR | ENST00000003084.11 | c.3038C>A | p.Pro1013His | missense_variant | 19/27 | 1 | NM_000492.4 | P2 | |
ENST00000456270.1 | n.178-5579G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152012Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251138Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135732
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461206Hom.: 0 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 726912
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152012Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74238
ClinVar
Submissions by phenotype
Cystic fibrosis Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2023 | The p.P1013H variant (also known as c.3038C>A), located in coding exon 19 of the CFTR gene, results from a C to A substitution at nucleotide position 3038. The proline at codon 1013 is replaced by histidine, an amino acid with similar properties. This variant has been reported in the heterozygous state in individuals undergoing preimplantation genetic diagnosis for cystic fibrosis (Girardet A et al. Clin. Genet., 2015 Feb;87:124-32; Girardet A et al. Eur. J. Hum. Genet., 2016 Apr;24:469-78; Capalbo A et al. PLoS Genet., 2019 10;15:e1008409). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 08, 2022 | This sequence change replaces proline, which is neutral and non-polar, with histidine, which is basic and polar, at codon 1013 of the CFTR protein (p.Pro1013His). This variant is present in population databases (rs193922516, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with CFTR-related conditions. ClinVar contains an entry for this variant (Variation ID: 35859). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 08, 2022 | PP3, PM2 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 18, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | May 21, 2021 | The CFTR c.3038C>A; p.Pro1013His variant (rs193922516) is reported in the literature in heterozygous carriers (Capalbo 2019, Girardet 2016), and has been reported with another CFTR variant in one 13 month old child with pancreatic insufficiency, normal lung function, and intermediate sweat chloride levels (SickKids CFTR database). This variant is also reported in ClinVar (Variation ID: 35859), and is only observed on nine alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. The proline at residue 1013 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.862). However, due to limited clinical and functional information, the significance of the p.Pro1013His variant is uncertain at this time. References: Link to SickKids CFTR database: http://www.genet.sickkids.on.ca/cftr/MutationDetailPage.external?sp=1372 Capalbo A et al. Optimizing clinical exome design and parallel gene-testing for recessive genetic conditions in preconception carrier screening: Translational research genomic data from 14,125 exomes. PLoS Genet. 2019 Oct 7;15(10):e1008409. PMID: 31589614. Girardet A et al. The improvement of the best practice guidelines for preimplantation genetic diagnosis of cystic fibrosis: toward an international consensus. Eur J Hum Genet. 2016 Apr;24(4):469-78. PMID: 26014425. - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 15, 2022 | Variant summary: CFTR c.3038C>A (p.Pro1013His) results in a non-conservative amino acid change located in the ABC transporter type 1, transmembrane domain (IPR011527) of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 251138 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. Although the variant has been reported in the literature in at least one heterozygous individual undergoing carrier screening analysis as part of preimplantation genetic diagnosis for Cystic Fibrosis (e.g. Girardet_2015), to our knowledge, no occurrence of c.3038C>A in individuals affected with Cystic Fibrosis and no experimental evidence demonstrating its impact on protein function have been reported in the peer-reviewed literature. One database (SickKids) reports this variant in a patient with intermediate sweat chloride levels. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
CFTR-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Aug 29, 2018 | - - |
Cystic fibrosis;C0238339:Hereditary pancreatitis;C0403814:Congenital bilateral aplasia of vas deferens from CFTR mutation;C2749757:Bronchiectasis with or without elevated sweat chloride 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 15, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at