ClinVar Miner

Submissions for variant NM_000492.4(CFTR):c.1499G>A (p.Gly500Asp)

gnomAD frequency: 0.00001  dbSNP: rs774945680
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000373122 SCV000344798 uncertain significance not provided 2016-08-12 criteria provided, single submitter clinical testing
Mendelics RCV000757859 SCV000886371 uncertain significance Cystic fibrosis 2018-11-05 criteria provided, single submitter clinical testing
Johns Hopkins Genomics, Johns Hopkins University RCV000757859 SCV001762363 uncertain significance Cystic fibrosis 2021-07-07 criteria provided, single submitter clinical testing CFTR c.1499G>A has been identified in 2 individuals with features of cystic fibrosis. This CFTR variant (rs774945680) is rare (<0.1%) in a large population dataset (gnomAD: 2/251288 total alleles; 0.0008%; no homozygotes) and has been reported in ClinVar (Variation ID: 290277). Three bioinformatic tools queried predict that this substitution would be damaging and the glycine residue at this position is evolutionarily conserved across all species assessed. We consider the clinical significance of CFTR c.1499G>A to be uncertain at this time.
Genome-Nilou Lab RCV000757859 SCV002027413 uncertain significance Cystic fibrosis 2021-09-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000757859 SCV002303349 uncertain significance Cystic fibrosis 2022-09-18 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 500 of the CFTR protein (p.Gly500Asp). This variant is present in population databases (rs774945680, 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: 290277). 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 not expected to disrupt CFTR protein function. 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000757859 SCV002500257 likely pathogenic Cystic fibrosis 2024-09-09 criteria provided, single submitter clinical testing Variant summary: CFTR c.1499G>A (p.Gly500Asp) results in a non-conservative amino acid change located in the first ATP-binding domain (IPR003439) 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 8e-06 in 251288 control chromosomes (gnomAD). The variant, listed as p.G500D, has been reported in the literature in individuals affected with Cystic Fibrosis (Sabino_2015, Martinez-Hernandez_2024, and in ClinVar, Accession: SCV002701322.2). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect resulted in approximately (Gt channel conductance) ~6% of normal chloride channel conductance relative to wild type (Bihler_2024). The following publications have been ascertained in the context of this evaluation (PMID: 25459562, 38388235, 38601560). ClinVar contains an entry for this variant (Variation ID: 290277). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Ambry Genetics RCV000757859 SCV002701322 pathogenic Cystic fibrosis 2020-08-31 criteria provided, single submitter clinical testing The p.G500D pathogenic mutation (also known as c.1499G>A), located in coding exon 11 of the CFTR gene, results from a G to A substitution at nucleotide position 1499. The glycine at codon 500 is replaced by aspartic acid, an amino acid with similar properties. In our internal cohort, this alteration was identified in trans with p.F508del mutation in an individual with cystic fibrosis (CF) (Ambry internal data). This mutation was also reported in conjugation with p.G542* in another individual with CF; however, the phase was not provided (Sabino R et al. J. Cyst. Fibros., 2015 Jul;14:474-81). In addition, internal structural analysis revealed that this alteration is more destabilizing than known pathogenic variants within the same domain (Flachowsky S et al. Zentralbl Gynakol, 1986;108:383-5). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
PreventionGenetics, part of Exact Sciences RCV004543136 SCV004800061 uncertain significance CFTR-related disorder 2024-01-17 no assertion criteria provided clinical testing The CFTR c.1499G>A variant is predicted to result in the amino acid substitution p.Gly500Asp. This variant was reported in the compound heterozygous state in an individual with cystic fibrosis (Sabino et al 2014. PubMed ID: 25459562). This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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