NM_017780.4(CHD7):c.6070C>T (p.Arg2024Ter) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 13, 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:: RCV004026047.1

Allele description [Variation Report for NM_017780.4(CHD7):c.6070C>T (p.Arg2024Ter)]

NM_017780.4(CHD7):c.6070C>T (p.Arg2024Ter)

Gene:

CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q12.2

Genomic location:

Preferred name:

NM_017780.4(CHD7):c.6070C>T (p.Arg2024Ter)

HGVS:

NC_000008.11:g.60852673C>T
NG_007009.1:g.178894C>T
NM_001316690.1:c.1717-9556C>T
NM_017780.4:c.6070C>TMANE SELECT
NP_060250.2:p.Arg2024Ter
LRG_176t1:c.6070C>T
LRG_176:g.178894C>T
NC_000008.10:g.61765232C>T
NM_017780.2:c.6070C>T
NM_017780.3:c.6070C>T

Protein change:

R2024*

Links:

dbSNP: rs1360515765

NCBI 1000 Genomes Browser:

rs1360515765

Molecular consequence:

NM_001316690.1:c.1717-9556C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_017780.4:c.6070C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

Recent activity

Clear Turn Off Turn On

cytochrome oxidase subunit I, partial (mitochondrion) [Moina micrura]
cytochrome oxidase subunit I, partial (mitochondrion) [Moina micrura]
gi|1009658480|gb|AMR72706.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004923872	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Nov 13, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 15300250, 19021638, 20624498, 23024289, 35938004 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004923872

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Nov 13, 2023)

germline

clinical testing

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in a new member of the chromodomain gene family cause CHARGE syndrome.

Vissers LE, van Ravenswaaij CM, Admiraal R, Hurst JA, de Vries BB, Janssen IM, van der Vliet WA, Huys EH, de Jong PJ, Hamel BC, Schoenmakers EF, Brunner HG, Veltman JA, van Kessel AG.

Nat Genet. 2004 Sep;36(9):955-7. Epub 2004 Aug 8.

PubMed [citation]

PMID:: 15300250

CHD7 mutations in patients initially diagnosed with Kallmann syndrome--the clinical overlap with CHARGE syndrome.

Jongmans MC, van Ravenswaaij-Arts CM, Pitteloud N, Ogata T, Sato N, Claahsen-van der Grinten HL, van der Donk K, Seminara S, Bergman JE, Brunner HG, Crowley WF Jr, Hoefsloot LH.

Clin Genet. 2009 Jan;75(1):65-71. doi: 10.1111/j.1399-0004.2008.01107.x. Epub 2008 Nov 17.

PubMed [citation]

PMID:: 19021638
PMCID:: PMC2854009

See all PubMed Citations (5)

Details of each submission

From Ambry Genetics, SCV004923872.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

The c.6070C>T (p.R2024*) alteration, located in exon 30 (coding exon 29) of the CHD7 gene, consists of a C to T substitution at nucleotide position 6070. This changes the amino acid from a arginine (R) to a stop codon at amino acid position 2024. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been reported in multiple individuals with features consistent with CHARGE syndrome (Vissers, 2004; Legendre, 2012), including multiple de novo occurrences (Jongmans, 2009; Wessels, 2010; Wu, 2022). Based on the available evidence, this alteration is classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine