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NM_000492.4(CFTR):c.1625G>A (p.Gly542Glu) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 31, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003324095.2

Allele description [Variation Report for NM_000492.4(CFTR):c.1625G>A (p.Gly542Glu)]

NM_000492.4(CFTR):c.1625G>A (p.Gly542Glu)

Genes:
CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]
LOC111674475:CFTR intron 11 enhancer [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
7q31.2
Genomic location:
Preferred name:
NM_000492.4(CFTR):c.1625G>A (p.Gly542Glu)
HGVS:
  • NC_000007.14:g.117587779G>A
  • NG_016465.4:g.126996G>A
  • NG_056131.3:g.734G>A
  • NM_000492.4:c.1625G>AMANE SELECT
  • NP_000483.3:p.Gly542Glu
  • NP_000483.3:p.Gly542Glu
  • LRG_663t1:c.1625G>A
  • LRG_663:g.126996G>A
  • LRG_663p1:p.Gly542Glu
  • NC_000007.13:g.117227833G>A
  • NM_000492.3:c.1625G>A
Protein change:
G542E
Molecular consequence:
  • NM_000492.4:c.1625G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004028732Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Jul 31, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004028732.1

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

Description

Variant summary: CFTR c.1625G>A (p.Gly542Glu) results in a non-conservative amino acid change located in the ATP-binding domain (IPR003439) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 250934 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1625G>A in individuals affected with Cystic Fibrosis has been reported. At least one publication reports experimental evidence evaluating an impact on protein function, finding no damaging effect of the variant on chloride channel conductance in vitro relative to wild type (e.g., Bihler_2023 (bioRxiv, no PMID)). One submitter has reported clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: May 1, 2024