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NM_000492.4(CFTR):c.1393-1G>A AND CFTR-related disorder

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Dec 30, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001831726.3

Allele description [Variation Report for NM_000492.4(CFTR):c.1393-1G>A]

NM_000492.4(CFTR):c.1393-1G>A

Genes:
CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]
CFTR-AS1:CFTR antisense RNA 1 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q31.2
Genomic location:
Preferred name:
NM_000492.4(CFTR):c.1393-1G>A
Other names:
1525-1G->A
HGVS:
  • NC_000007.14:g.117559463G>A
  • NG_016465.4:g.98680G>A
  • NM_000492.4:c.1393-1G>AMANE SELECT
  • LRG_663t1:c.1393-1G>A
  • LRG_663:g.98680G>A
  • NC_000007.13:g.117199517G>A
  • NM_000492.3:c.1393-1G>A
Links:
dbSNP: rs397508200
NCBI 1000 Genomes Browser:
rs397508200
Molecular consequence:
  • NM_000492.4:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
CFTR-related disorder (CFTR-RD)
Synonyms:
CFTR-related disorders; CFTR-related condition
Identifiers:
MedGen: C5924204

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002080586Natera, Inc.
no assertion criteria provided
Pathogenic
(Mar 17, 2017) 		germlineclinical testing

SCV004718913PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Dec 30, 2023) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From Natera, Inc., SCV002080586.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From PreventionGenetics, part of Exact Sciences, SCV004718913.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The CFTR c.1393-1G>A variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant, previously described as c.1525-1G>A using legacy nomenclature, has been reported to be causative for cystic fibrosis (Castellani et al. 2008. PubMed ID: 18456578; Supplemental table 2, Sosnay et al. 2013. PubMed ID: 23974870). The c.1393-1G>A variant has also been reported in patient with idiopathic chronic pancreatitis who had a corresponding pathogenic variant in the SPINK1 gene (Supplemental table 1, Midha et al. 2010. PubMed ID: 20551465). This variant is reported in 0.026% of alleles in individuals of South Asian descent in gnomAD. Variants that disrupt the consensus splice acceptor site in CFTR are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Nov 24, 2024