NM_017780.4(CHD7):c.6079C>T (p.Arg2027Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Sep 15, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_017780.4(CHD7):c.6079C>T (p.Arg2027Ter)]

NM_017780.4(CHD7):c.6079C>T (p.Arg2027Ter)

CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_017780.4(CHD7):c.6079C>T (p.Arg2027Ter)
  • NC_000008.11:g.60852682C>T
  • NG_007009.1:g.178903C>T
  • NM_001316690.1:c.1717-9547C>T
  • NM_017780.4:c.6079C>TMANE SELECT
  • NP_060250.2:p.Arg2027Ter
  • LRG_176t1:c.6079C>T
  • LRG_176:g.178903C>T
  • NC_000008.10:g.61765241C>T
  • NM_017780.2:c.6079C>T
  • NM_017780.3:c.6079C>T
  • p.[Arg2027*]
Protein change:
dbSNP: rs886040995
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001316690.1:c.1717-9547C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_017780.4:c.6079C>T - nonsense - [Sequence Ontology: SO:0001587]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000329270GeneDxcriteria provided, single submitter
(Sep 15, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000329270.5

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


The R2027X nonsense variant in the CHD7 gene has been reported previously as a de novo occurrence in four patients in association with CHARGE syndrome (Jongmans et al., 2006; Janssen et al., 2012; Busa et al., 2016). Approximately 45% of CHD7 pathogenic variants are nonsense changes predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay (Janssen et al., 2012; Zentner et al, 2010). Additionally, the R2027X variant was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Therefore, the presence of the R2027X pathogenic variant is consistent with a diagnosis of CHARGE syndrome

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

Last Updated: May 10, 2021

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