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NM_000492.4(CFTR):c.2079T>G (p.Phe693Leu) AND CFTR-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 21, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004537370.1

Allele description [Variation Report for NM_000492.4(CFTR):c.2079T>G (p.Phe693Leu)]

NM_000492.4(CFTR):c.2079T>G (p.Phe693Leu)

Gene:
CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q31.2
Genomic location:
Preferred name:
NM_000492.4(CFTR):c.2079T>G (p.Phe693Leu)
HGVS:
  • NC_000007.14:g.117592246T>G
  • NG_016465.4:g.131463T>G
  • NM_000492.4:c.2079T>GMANE SELECT
  • NP_000483.3:p.Phe693Leu
  • NP_000483.3:p.Phe693Leu
  • LRG_663t1:c.2079T>G
  • LRG_663:g.131463T>G
  • LRG_663p1:p.Phe693Leu
  • NC_000007.13:g.117232300T>G
  • NM_000492.3:c.2079T>G
  • P13569:p.Phe693Leu
Protein change:
F693L
Links:
UniProtKB: P13569#VAR_000213; dbSNP: rs145540754
NCBI 1000 Genomes Browser:
rs145540754
Molecular consequence:
  • NM_000492.4:c.2079T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
CFTR-related disorder (CFTR-RD)
Synonyms:
CFTR-related disorders; CFTR-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004115531PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Nov 21, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004115531.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The CFTR c.2079T>G variant is predicted to result in the amino acid substitution p.Phe693Leu. This variant has been reported with a minor allele frequency as high as 0.12% in African populations including one homozygous individual (http://gnomad.broadinstitute.org/variant/7-117232300-T-G), and has been reported as likely benign and a variant of uncertain significance in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/194336/). The c.2079T>G variant has been reported in a CFTR database with the patient presenting with severe asthma (http://www.genet.sickkids.on.ca/MutationDetailPage.external?sp=1209). A different nucleotide substitution, c.2077T>C, resulting in the same amino acid change (p.Phe693Leu) has been reported in a patient with pancreatic insufficiency (http://www.genet.sickkids.on.ca/MutationDetailPage.external?sp=343). This variant has been reported individuals with cystic fibrosis (Groman et al. 2002. PubMed ID: 12167682; Mutesa et al. 2008. PubMed ID: 19017867), pancreatic insufficient cystic fibrosis (Boyne et al. 2000. PubMed ID: 10970190), and healthy individuals (Vankeerberghen et al. 1998. PubMed ID: 9736778). Functional studies have shown that the p.Phe693Leu variant did not significantly affect chloride transport when compared to wild-type CFTR channels (Vankeerberghen et al. 1998. PubMed ID: 9736778). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024