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NM_000492.4(CFTR):c.2042A>T (p.Glu681Val) AND Cystic fibrosis

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Nov 10, 2022
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:
RCV001273210.16

Allele description [Variation Report for NM_000492.4(CFTR):c.2042A>T (p.Glu681Val)]

NM_000492.4(CFTR):c.2042A>T (p.Glu681Val)

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.2042A>T (p.Glu681Val)
HGVS:
  • NC_000007.14:g.117592209A>T
  • NG_016465.4:g.131426A>T
  • NM_000492.4:c.2042A>TMANE SELECT
  • NP_000483.3:p.Glu681Val
  • NP_000483.3:p.Glu681Val
  • LRG_663t1:c.2042A>T
  • LRG_663:g.131426A>T
  • LRG_663p1:p.Glu681Val
  • NC_000007.13:g.117232263A>T
  • NM_000492.3:c.2042A>T
  • NM_000492.4:c.2042A>T
Protein change:
E681V
Links:
dbSNP: rs201295415
NCBI 1000 Genomes Browser:
rs201295415
Molecular consequence:
  • NM_000492.4:c.2042A>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001174878Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Likely benign
(Nov 10, 2022)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link,

SCV001455986Natera, Inc.
no assertion criteria provided
Uncertain significance
(Apr 23, 2018)
germlineclinical testing

SCV002027436Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Sep 5, 2021)
germlineclinical testing

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

SCV002988491Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Sep 7, 2022)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Pulmonary nontuberculous mycobacterial disease: prospective study of a distinct preexisting syndrome.

Kim RD, Greenberg DE, Ehrmantraut ME, Guide SV, Ding L, Shea Y, Brown MR, Chernick M, Steagall WK, Glasgow CG, Lin J, Jolley C, Sorbara L, Raffeld M, Hill S, Avila N, Sachdev V, Barnhart LA, Anderson VL, Claypool R, Hilligoss DM, Garofalo M, et al.

Am J Respir Crit Care Med. 2008 Nov 15;178(10):1066-74. doi: 10.1164/rccm.200805-686OC. Epub 2008 Aug 14.

PubMed [citation]
PMID:
18703788
PMCID:
PMC2720143

Association of CFTR gene variants with nontuberculous mycobacterial lung disease in a Korean population with a low prevalence of cystic fibrosis.

Jang MA, Kim SY, Jeong BH, Park HY, Jeon K, Kim JW, Ki CS, Koh WJ.

J Hum Genet. 2013 May;58(5):298-303. doi: 10.1038/jhg.2013.19. Epub 2013 Mar 21.

PubMed [citation]
PMID:
23514810
See all PubMed Citations (7)

Details of each submission

From Ambry Genetics, SCV001174878.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

From Natera, Inc., SCV001455986.1

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

From Genome-Nilou Lab, SCV002027436.1

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002988491.1

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

Description

This sequence change replaces glutamic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 681 of the CFTR protein (p.Glu681Val). This variant is present in population databases (rs201295415, gnomAD 0.2%). This missense change has been observed in individual(s) with chronic pancreatitis (PMID: 29173301). ClinVar contains an entry for this variant (Variation ID: 287205). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 13, 2024