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NM_000492.3(CFTR):c.220C>T (p.Arg74Trp) AND not specified

Germline classification:
Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:
Feb 14, 2017
Review status:
criteria provided, conflicting classifications
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:
RCV000479747.1

Allele description

NM_000492.3(CFTR):c.220C>T (p.Arg74Trp)

Gene:
CFTR:cystic fibrosis transmembrane conductance regulator [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q31.2
Genomic location:
Preferred name:
NM_000492.3(CFTR):c.220C>T (p.Arg74Trp)
HGVS:
  • NC_000007.14:g.117509089C>T
  • NG_016465.4:g.48306C>T
  • NM_000492.3:c.220C>T
  • NP_000483.3:p.Arg74Trp
  • LRG_663t1:c.220C>T
  • LRG_663:g.48306C>T
  • LRG_663p1:p.Arg74Trp
  • NC_000007.13:g.117149143C>T
  • P13569:p.Arg74Trp
Protein change:
R74W
Links:
UniProtKB: P13569#VAR_000110; dbSNP: rs115545701
NCBI 1000 Genomes Browser:
rs115545701
Molecular consequence:
  • NM_000492.3:c.220C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000568547GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Uncertain significance
(Jun 10, 2016)
germlineclinical testing

Citation Link,

SCV000602984ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)
Pathogenic
(Feb 14, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000568547.3

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

Description

The R74W variant in the CFTR gene has been reported previously as heterozygous in one individual with CF; no other variants in the CFTR gene were identified in this individual (Claustres et al., 1993). Expression studies in FRT cells showed that D1270N transfected cells displayed decreased chloride transport activity compared to wild type cells (Van Goor et al., 2014). However, an earlier functional study in HeLa cells showed that D1270N transfected cells displayed chloride transport kinetics similar to wild type cells (Fanen et al., 1999). The R74W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position where amino acids with similar properties to Arginine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret R74W as a variant of uncertain significance.

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

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV000602984.1

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

Last Updated: Feb 8, 2019