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

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 26, 2019
Accession:
VCV000267435.7
Variation ID:
267435
Description:
single nucleotide variant
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NM_017780.4(CHD7):c.6079C>T (p.Arg2027Ter)

Allele ID
262660
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8q12.2
Genomic location
8: 60852682 (GRCh38) GRCh38 UCSC
8: 61765241 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.61765241C>T
NC_000008.11:g.60852682C>T
NM_017780.4:c.6079C>T MANE Select NP_060250.2:p.Arg2027Ter nonsense
... more HGVS
Protein change
R2027*
Other names
-
Canonical SPDI
NC_000008.11:60852681:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10602502
dbSNP: rs886040995
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 6 criteria provided, multiple submitters, no conflicts Oct 26, 2019 RCV000258088.6
Pathogenic 1 criteria provided, single submitter Sep 15, 2016 RCV000330520.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CHD7 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1607 1635

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Sep 05, 2016)
criteria provided, single submitter
()
Method: clinical testing
CHARGE syndrome
Allele origin: germline
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia
Accession: SCV000328344.1
Submitted: (Oct 24, 2016)
Comment:
Clinical Testing
Evidence details
Pathogenic
(-)
criteria provided, single submitter
Method: research
CHARGE association
(Autosomal dominant inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Study: Broad Institute Center for Mendelian Genomics (CMG)
Accession: SCV000786713.1
Submitted: (Jun 27, 2018)
Evidence details
Comment:
The heterozygous p.Arg227Ter variant was identified by our study in one individual with CHARGE syndrome. The p.Arg227Ter variant is believed to be pathogenic based on … (more)
Pathogenic
(Sep 15, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000329270.5
Submitted: (Jan 29, 2019)
Evidence details
Comment:
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 … (more)
Pathogenic
(Apr 26, 2018)
criteria provided, single submitter
Method: clinical testing
CHARGE association
Allele origin: unknown
Victorian Clinical Genetics Services,Murdoch Childrens Research Institute
Accession: SCV001244805.1
Submitted: (Aug 15, 2019)
Evidence details
Comment:
A heterozygous nonsense variant, NM_017780.3(CHD7):c.6079C>T, has been identified in exon 30 of 38 in the CHD7 gene. The variant is predicted to result in a … (more)
Pathogenic
(Oct 26, 2019)
criteria provided, single submitter
Method: clinical testing
CHARGE association
Allele origin: germline
Invitae
Accession: SCV000755717.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Arg2027*) in the CHD7 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Oct 27, 2017)
no assertion criteria provided
Method: research
CHARGE association
Allele origin: de novo
SBielas Lab, Department of Human Genetics,University of Michigan
Accession: SCV000680052.1
Submitted: (Oct 30, 2017)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(-)
no assertion criteria provided
Method: research
CHARGE syndrome
Allele origin: de novo
University of Washington Center for Mendelian Genomics, University of Washington
Accession: SCV001197958.1
Submitted: (Nov 05, 2019)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Genetic analysis of CHARGE syndrome identifies overlapping molecular biology. Moccia A Genetics in medicine : official journal of the American College of Medical Genetics 2018 PMID: 29300383
Prenatal findings in children with early postnatal diagnosis of CHARGE syndrome. Busa T Prenatal diagnosis 2016 PMID: 27061523
The prevalence of CHD7 missense versus truncating mutations is higher in patients with Kallmann syndrome than in typical CHARGE patients. Marcos S The Journal of clinical endocrinology and metabolism 2014 PMID: 25077900
Mutation update on the CHD7 gene involved in CHARGE syndrome. Janssen N Human mutation 2012 PMID: 22461308
CHARGE syndrome: the phenotypic spectrum of mutations in the CHD7 gene. Jongmans MC Journal of medical genetics 2006 PMID: 16155193

Text-mined citations for rs886040995...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 10, 2021