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NM_000492.3(CFTR):c.1521_1523del (p.Phe508del) AND not provided

Germline classification:
Pathogenic (21 submissions)
Last evaluated:
Aug 1, 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:
RCV000058929.82

Allele description [Variation Report for NM_000492.3(CFTR):c.1521_1523del (p.Phe508del)]

NM_000492.3(CFTR):c.1521_1523del (p.Phe508del)

Genes:
CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]
CFTR-AS1:CFTR antisense RNA 1 [Gene - HGNC]
Variant type:
Deletion
Cytogenetic location:
7q31.2
Genomic location:
Preferred name:
NM_000492.3(CFTR):c.1521_1523del (p.Phe508del)
Other names:
F508del; deltaF508; F508delF; DF508; Phe508del; DeltaF508; [delta]F508
HGVS:
  • NC_000007.13:g.117199645_117199647del
  • NC_000007.14:g.117559592_117559594del
  • NG_016465.4:g.98809_98811del
  • NM_000492.4:c.1521_1523delMANE SELECT
  • NP_000483.3:p.Phe508del
  • NP_000483.3:p.Phe508del
  • LRG_663t1:c.1521_1523del
  • LRG_663:g.98809_98811del
  • LRG_663p1:p.Phe508del
  • NC_000007.13:g.117199645_117199647del
  • NC_000007.13:g.117199646_117199648del
  • NC_000007.13:g.117199646_117199648del
  • NC_000007.13:g.117199646_117199648delCTT
  • NC_000007.14:g.117559592_117559594del
  • NC_000007.14:g.117559592_117559594delCTT
  • NG_016465.1:g.84630_84632delCTT
  • NM_000492.3:c.1520_1522del
  • NM_000492.3:c.1520_1522delTCT
  • NM_000492.3:c.1521_1523del
  • NM_000492.3:c.1521_1523delCTT
  • NM_000492.4:c.1520_1522delMANE SELECT
  • NM_000492.4:c.1520_1522delTCTMANE SELECT
  • NM_000492.4:c.1521_1523delCTTMANE SELECT
Protein change:
PHE508DEL
Links:
PharmGKB Clinical Annotation: 981755820; OMIM: 602421.0001; dbSNP: rs113993960
NCBI 1000 Genomes Browser:
rs113993960
Molecular consequence:
  • NM_000492.4:c.1521_1523del - inframe_deletion - [Sequence Ontology: SO:0001822]
Functional consequence:
loss_of_function_variant [Sequence Ontology: SO:0002054]
Observations:
633

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000090450SNPedia
no classification provided
not providedgermlinenot provided

SCV000329246GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Pathogenic
(Jul 30, 2018)
germlineclinical testing

Citation Link,

SCV000330918Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions)
Pathogenic
(Jan 3, 2017)
germlineclinical testing

Citation Link,

SCV000511517Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 28, 2016)
germlineclinical testing

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

SCV000889288Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Pathogenic
(Feb 17, 2020)
unknownclinical testing

PubMed (161)
[See all records that cite these PMIDs]

SCV000928113Blueprint Genetics
criteria provided, single submitter

(Blueprint Genetics Variant Classification Scheme)
Pathogenic
(Dec 12, 2018)
germlineclinical testing

Citation Link,

SCV001246813CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Aug 1, 2024)
germlineclinical testing

Citation Link,

SCV001251746Genomic Research Center, Shahid Beheshti University of Medical Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 3, 2020)
unknownclinical testing

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

SCV001450105Clinical Genetics and Genomics, Karolinska University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 29, 2014)
germlineclinical testing

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

SCV001553614Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Pathogenicunknownclinical testing

SCV001713417Mayo Clinic Laboratories, Mayo Clinic
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 31, 2023)
germlineclinical testing

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

Citation Link,

SCV001744105Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001929598Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV002009133Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 3, 2021)
germlineclinical testing

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

SCV002019253Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 15, 2023)
germlineclinical testing

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

SCV002035293Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV002048630ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Pathogenic
(Oct 19, 2023)
germlineclinical testing

Citation Link,

SCV002502414AiLife Diagnostics, AiLife Diagnostics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 30, 2022)
germlineclinical testing

PubMed (41)
[See all records that cite these PMIDs]

SCV002818128Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 17, 2022)
germlineclinical testing

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

SCV004242533Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 31, 2024)
germlineclinical testing

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

SCV005197698Clinical Genetics Laboratory, Skane University Hospital Lund
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 11, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownnonot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes105not providednot providednot providednot providedclinical testing
not providedgermlineunknown528not providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing, literature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Applying Cystic Fibrosis Transmembrane Conductance Regulator Genetics and CFTR2 Data to Facilitate Diagnoses.

Sosnay PR, Salinas DB, White TB, Ren CL, Farrell PM, Raraigh KS, Girodon E, Castellani C.

J Pediatr. 2017 Feb;181S:S27-S32.e1. doi: 10.1016/j.jpeds.2016.09.063.

PubMed [citation]
PMID:
28129809

∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis.

Pankow S, Bamberger C, Calzolari D, Martínez-Bartolomé S, Lavallée-Adam M, Balch WE, Yates JR 3rd.

Nature. 2015 Dec 24;528(7583):510-6. doi: 10.1038/nature15729. Epub 2015 Nov 30.

PubMed [citation]
PMID:
26618866
PMCID:
PMC4826614
See all PubMed Citations (162)

Details of each submission

From SNPedia, SCV000090450.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV000329246.6

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

Description

The c.1521_1523delCTT pathogenic variant in the CFTR gene (also known as p.Phe508del or delta F508) is the most common variant identified in the CFTR gene, with up to 90% of individuals with cystic fibrosis (CF) having at least one copy of the c.1521_1523delCTT variant (Cai et al., 2011). The c.1521_1523delCTT variant results in an in-frame deletion of a single Phenylalanine residue at codon 508. Individuals who are homozygous for the c.1521_1523delCTT variant demonstrate the classic features of CF, whereas individuals compound heterozygous for the c.1521_1523delCTT variant and another CFTR variant may have a modified disease phenotype (Ong et al., 2017). Heterozygous carriers of the c.1521_1523delCTT variant are usually asymptomatic, however, may be at increased risk for developing a CFTR-related disorder, as an increased prevalence of single CFTR pathogenic variants has been observed among individuals with chronic pulmonary conditions, CAVD and pancreatitis (Cuppens et al., 2004; Bombieri et al., 2011). We interpret the c.1521_1523delCTT variant as a pathogenic variant.

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

From Eurofins Ntd Llc (ga), SCV000330918.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided210not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided210not providednot providednot provided

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000511517.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.01539not providednot provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000889288.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (161)

Description

The c.1521_1523del (p.Phe508del or Delta F508) pathogenic variant is an in-frame deletion of the phenylalanine amino acid at position p.508 of the CFTR protein. It is the most common cystic fibrosis pathogenic variant that accounts for approximately 70% of alleles in affected patients and causes a severe phenotype due to deleterious effects on CFTR protein maturation and function (PMID: 23857699 (2013), 23974870 (2013), 25148434 (2014), and 26581802 (2016)). Based on the available information, this variant is classified as pathogenic.

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

From Blueprint Genetics, SCV000928113.1

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

From CeGaT Center for Human Genetics Tuebingen, SCV001246813.26

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided73not providednot providedclinical testingnot provided

Description

CFTR: PM3:Very Strong, PS3:Moderate, PM2:Supporting, PM4:Supporting

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided73not providednot providednot provided

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV001251746.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnonot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics and Genomics, Karolinska University Hospital, SCV001450105.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided27not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided27not providednot providednot provided

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001553614.1

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

Description

The CFTR p.F508del variant is the most common variant known to cause cystic fibrosis (CF); this variant acounts for ~70% of CFTR variants and is present in approximately 85% of CF patients worldwide (Maiuri_2015_PMID:26046070). The variant was identified in dbSNP (ID: rs113993960) and ClinVar (classified as pathogenic by the American College of Medical Genetics and Genomics, Laboratory for Molecular Medicine and 20+ other laboratories). The variant was identified in control databases in 2027 of 282630 chromosomes (1 homozygous) at a frequency of 0.007172 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 1598 of 129034 chromosomes (freq: 0.01238), Other in 49 of 7214 chromosomes (freq: 0.006792), Ashkenazi Jewish in 58 of 10368 chromosomes (freq: 0.005594), Latino in 135 of 35426 chromosomes (freq: 0.003811), African in 65 of 24958 chromosomes (freq: 0.002604), European (Finnish) in 61 of 25074 chromosomes (freq: 0.002433) and South Asian in 61 of 30608 chromosomes (freq: 0.001993), but was not observed in the East Asian population. This variant is an in-frame deletion resulting in the removal of a phenylalanine (F) residue at codon 508; the deletion of p.F508 results in a misfolded mutant protein that is prematurely degraded before it reaches the plasma membrane (Maiuri_2015_PMID:26046070). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV001713417.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided318not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided318not providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001744105.3

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001929598.1

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

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002009133.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV002019253.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV002035293.1

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002048630.7

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

Description

The CFTR c.1521_1523del; p.Phe508del (F508del) variant is the most common pathogenic CFTR variant that has been reported in Caucasians (Sosnay 2013, CFTR2 database). This variant is considered to cause cystic fibrosis when identified with another pathogenic variant on the opposite chromosome. REFERENCES CFTR2 database: http://cftr2.org/ Sosnay P 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.

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

From AiLife Diagnostics, AiLife Diagnostics, SCV002502414.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (41)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided5not providednot providednot provided

From Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital, SCV002818128.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV004242533.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005197698.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024