NM_000492.4(CFTR):c.1585-1G>A AND not provided

Germline classification:: Pathogenic (10 submissions)
Last evaluated:: May 24, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000224919.37

Allele description [Variation Report for NM_000492.4(CFTR):c.1585-1G>A]

NM_000492.4(CFTR):c.1585-1G>A

Genes:

CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]
LOC111674475:CFTR intron 11 enhancer [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

7q31.2

Genomic location:

Preferred name:

NM_000492.4(CFTR):c.1585-1G>A

Other names:

1717-1G->A; 1717-1>A

HGVS:

NC_000007.14:g.117587738G>A
NG_016465.4:g.126955G>A
NG_056131.3:g.693G>A
NM_000492.3(CFTR):c.1585-1G>A
NM_000492.4:c.1585-1G>AMANE SELECT
LRG_663t1:c.1585-1G>A
LRG_663:g.126955G>A
NC_000007.13:g.117227792G>A
NM_000492.3:c.1585-1G>A
NM_000492.4:c.1585-1G>A

Nucleotide change:

1717-1G>A

Links:

Genetic Testing Registry (GTR): GTR000074114; Genetic Testing Registry (GTR): GTR000500233; OMIM: 602421.0008; dbSNP: rs76713772

Molecular consequence:

NM_000492.4:c.1585-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000281124	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 24, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000322328	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Oct 26, 2018)	germline	clinical testing	Citation Link,
SCV000603007	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Pathogenic (Nov 10, 2023)	germline	clinical testing	Citation Link,
SCV000854844	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Pathogenic (Mar 28, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001134116	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	pathogenic (May 22, 2024)	unknown	clinical testing	PubMed (17) [See all records that cite these PMIDs] 29261177, 31036917, 31589614, 31345219, 36007526, 37175647, 34782259, 34996830, 2210769, 2236053, 1757966, 7689009, 15371902, 23974870, 25066652, 26708955, 26467025
SCV001713421	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 24, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001739956	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001955455	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001974900	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV002019218	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 26, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	5	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Reproductive genetic carrier screening for cystic fibrosis, fragile X syndrome, and spinal muscular atrophy in Australia: outcomes of 12,000 tests.

Archibald AD, Smith MJ, Burgess T, Scarff KL, Elliott J, Hunt CE, McDonald Z, Barns-Jenkins C, Holt C, Sandoval K, Siva Kumar V, Ward L, Allen EC, Collis SV, Cowie S, Francis D, Delatycki MB, Yiu EM, Massie RJ, Pertile MD, du Sart D, Bruno D, et al.

Genet Med. 2018 Apr;20(5):513-523. doi: 10.1038/gim.2017.134. Epub 2017 Oct 26. Erratum in: Genet Med. 2018 Nov;20(11):1485. doi: 10.1038/gim.2017.266..

PubMed [citation]

PMID:: 29261177

Sequencing as a first-line methodology for cystic fibrosis carrier screening.

Beauchamp KA, Johansen Taber KA, Grauman PV, Spurka L, Lim-Harashima J, Svenson A, Goldberg JD, Muzzey D.

Genet Med. 2019 Nov;21(11):2569-2576. doi: 10.1038/s41436-019-0525-y. Epub 2019 Apr 30. Erratum in: Genet Med. 2019 Oct;21(10):2407-2408. doi: 10.1038/s41436-019-0543-9..

PubMed [citation]

PMID:: 31036917
PMCID:: PMC6831513

See all PubMed Citations (18)

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000281124.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.000407	not provided	not provided

From GeneDx, SCV000322328.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.1585-1G>A pathogenic variant in the CFTR gene is one of the common pathogenic variants associated with cystic fibrosis (Kerem et al., 1990; Hull et al., 1993; Ooi et al., 2012). This splice site variant destroys the canonical splice acceptor site in intron 11. Functional studies show this variant results in skipping of exon 12 with a frameshift that results in a premature termination codon, and the mRNA is not able to generate a stable protein product (Hull et al., 1993; Sharma et al., 2014). Although not present in the homozygous state, the NHLBI Exome Sequencing Project reports that c.1585-1G>A was observed in 12/8600 alleles (0.14%) from individuals of European American background, indicating it may be a rare variant in this population. We interpret c.1585-1G>A as a pathogenic variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000603007.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The CFTR c.1585-1G>A variant (rs76713772), also known as 1717-1G>A, has been reported in patients with the pancreatic insufficient form of cystic fibrosis (Guillermit 1990, Kerem 1990, Ivady 2011, Sosnay 2013). This variant is reported in ClinVar (Variation ID: 7112), is found in the non-Finnish European population with an allele frequency of 0.015% (19/128,796 alleles) in the Genome Aggregation Database. This variant disrupts the canonical splice acceptor site of intron 11, which is likely to negatively impact gene function. Based on available information, this variant is considered to be pathogenic. References: Guillermit H et al. A 3' splice site consensus sequence mutation in the cystic fibrosis gene. Hum Genet. 1990 85(4):450-3. PMID: 2210769 Ivady G et al. Distribution of CFTR mutations in Eastern Hungarians: relevance to genetic testing and to the introduction of newborn screening for cystic fibrosis. J Cyst Fibros. 2011 10(3):217-20. PMID: 21296036 Kerem B et al. Identification of mutations in regions corresponding to the two putative nucleotide (ATP)-binding folds of the cystic fibrosis gene. Proc Natl Acad Sci U S A. 1990 87(21):8447-51. PMID: 2236053 Sosnay PR et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet. 2013 45(10):1160-7. PMID: 23974870

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000854844.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		5	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001134116.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (17)

Description

The CFTR c.1585-1G>A (also known as 1717-1G>A) variant disrupts a canonical splice-acceptor site and interferes with normal CFTR mRNA splicing. This variant is associated with cystic fibrosis (CF) (PMIDs: 29261177 (2018), 31036917 (2019), and 34782259 (2021)), and has been reported along with other pathogenic CFTR variants in individuals with classic CF (PMID: 7689009 (1993)), pancreatic insufficiency (PMIDs: 2236053 (1990), 2210769 (1990), 1757966 (1991), and 23974870 (2013)) and in at least one individual with chronic obstructive pulmonary disease (PMID: 34996830 (2022)). Experimental studies have also shown that this variant results in exon 12 skipping and therefore disrupts protein production (PMIDs: 7689009 (1993), 23974870 (2013) and 25066652 (2014)). The frequency of this variant in the general population, 0.0002 (10/50648 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001713421.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001739956.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001955455.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001974900.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002019218.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 4, 2026

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