NM_000492.4(CFTR):c.2036G>A (p.Trp679Ter) AND Cystic fibrosis

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Apr 27, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000046525.5

Allele description [Variation Report for NM_000492.4(CFTR):c.2036G>A (p.Trp679Ter)]

NM_000492.4(CFTR):c.2036G>A (p.Trp679Ter)

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.2036G>A (p.Trp679Ter)
HGVS:
  • NC_000007.14:g.117592203G>A
  • NG_016465.4:g.131420G>A
  • NM_000492.4:c.2036G>AMANE SELECT
  • NP_000483.3:p.Trp679Ter
  • NP_000483.3:p.Trp679Ter
  • LRG_663t1:c.2036G>A
  • LRG_663:g.131420G>A
  • LRG_663p1:p.Trp679Ter
  • NC_000007.13:g.117232257G>A
  • NM_000492.3:c.2036G>A
Protein change:
W679*
Links:
dbSNP: rs397508333
NCBI 1000 Genomes Browser:
rs397508333
Molecular consequence:
  • NM_000492.4:c.2036G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Cystic fibrosis (CF)
Synonyms:
Mucoviscidosis
Identifiers:
MONDO: MONDO:0009061; MedGen: C0010674; Orphanet: 586; OMIM: 219700

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000221007Counsylcriteria provided, single submitter
Likely pathogenic
(Jan 6, 2015)
unknownliterature only

PubMed (3)
[See all records that cite these PMIDs]

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV001425428Johns Hopkins Genomics, Johns Hopkins Universitycriteria provided, single submitter
Pathogenic
(Apr 27, 2020)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene?

Dorfman R, Nalpathamkalam T, Taylor C, Gonska T, Keenan K, Yuan XW, Corey M, Tsui LC, Zielenski J, Durie P.

Clin Genet. 2010 May;77(5):464-73. doi: 10.1111/j.1399-0004.2009.01351.x. Epub 2009 Jan 6.

PubMed [citation]
PMID:
20059485

Comparing the American and European diagnostic guidelines for cystic fibrosis: same disease, different language?

Ooi CY, Dupuis A, Ellis L, Jarvi K, Martin S, Gonska T, Dorfman R, Kortan P, Solomon M, Tullis E, Durie PR.

Thorax. 2012 Jul;67(7):618-24. doi: 10.1136/thoraxjnl-2011-201454. Epub 2012 Apr 15.

PubMed [citation]
PMID:
22504961
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000221007.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Johns Hopkins Genomics, Johns Hopkins University, SCV001425428.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This CFTR variant has been previously reported in patients with cystic fibrosis and a single submitter in ClinVar classifies it as likely pathogenic (variation ID: 53429). This nonsense variant results in a premature stop codon in exon 14 (legacy exon 13) likely leading to nonsense-mediated decay and lack of protein production. We consider this variant to be pathogenic.

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

Last Updated: Dec 4, 2021

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