NM_000492.3(CFTR):c.1521_1523del (p.Phe508del) AND CFTR-related disorder

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Sep 26, 2024
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:: RCV001831519.15

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]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method
SCV002080609	Natera, Inc.	no assertion criteria provided	Pathogenic (Mar 17, 2017)	germline	clinical testing
SCV002507456	Genome Diagnostics Laboratory, The Hospital for Sick Children	no assertion criteria provided	Pathogenic (Oct 11, 2019)	germline	clinical testing
SCV004105952	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Pathogenic (Sep 26, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002080609

Natera, Inc.

no assertion criteria provided

Pathogenic
(Mar 17, 2017)

germline

clinical testing

SCV002507456

Genome Diagnostics Laboratory, The Hospital for Sick Children

no assertion criteria provided

Pathogenic
(Oct 11, 2019)

germline

clinical testing

SCV004105952

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Pathogenic
(Sep 26, 2024)

germline

clinical testing

Help

Summary from all submissions

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

Details of each submission

From Natera, Inc., SCV002080609.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, The Hospital for Sick Children, SCV002507456.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV004105952.3

#	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.1521_1523delCTT variant is predicted to result in an in-frame deletion (p.Phe508del). This variant, frequently described as ΔF508, is known to disrupt protein function and is the most common cause of autosomal recessive cystic fibrosis (Riordan et al. 1989. PubMed ID: 2475911; Watson et al. 2004. PubMed ID: 15371902; Sosnay et al. 2013. PubMed ID: 23974870). This variant is reported in 1.2% of alleles in individuals of European (Non-Finnish) descent. In summary, we classify this variant as pathogenic.

#	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: Oct 26, 2024

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