NM_017780.4(CHD7):c.1774_1778del (p.Gln592fs) AND CHARGE syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 5, 2021
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:: RCV001937212.4

Allele description [Variation Report for NM_017780.4(CHD7):c.1774_1778del (p.Gln592fs)]

NM_017780.4(CHD7):c.1774_1778del (p.Gln592fs)

Genes:

LOC126860403:CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:61693034-61694233 [Gene]
CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8q12.2

Genomic location:

Preferred name:

NM_017780.4(CHD7):c.1774_1778del (p.Gln592fs)

HGVS:

NC_000008.11:g.60781108_60781112del
NG_007009.1:g.107329_107333del
NM_001316690.1:c.1716+58_1716+62del
NM_017780.4:c.1774_1778delMANE SELECT
NP_060250.2:p.Gln592fs
LRG_176:g.107329_107333del
NC_000008.10:g.61693666_61693670del
NC_000008.10:g.61693667_61693671del

Protein change:

Q592fs

Links:

dbSNP: rs2150669316

NCBI 1000 Genomes Browser:

rs2150669316

Molecular consequence:

NM_017780.4:c.1774_1778del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001316690.1:c.1716+58_1716+62del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: CHARGE syndrome (CHARGE)
Synonyms:: CHARGE ASSOCIATION--COLOBOMA, HEART ANOMALY, CHOANAL ATRESIA, RETARDATION, GENITAL AND EAR ANOMALIES; Coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies; CHARGE association; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008965; MedGen: C0265354; Orphanet: 138; OMIM: 214800

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MED23 [Drosophila pseudoobscura]
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Gene ID:4805501

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LEMD2 LEM domain nuclear envelope protein 2 [Homo sapiens]
LEMD2 LEM domain nuclear envelope protein 2 [Homo sapiens]
Gene ID:221496

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002137030	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 5, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22461308, 25077900, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002137030

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 5, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Mutation update on the CHD7 gene involved in CHARGE syndrome.

Janssen N, Bergman JE, Swertz MA, Tranebjaerg L, Lodahl M, Schoots J, Hofstra RM, van Ravenswaaij-Arts CM, Hoefsloot LH.

Hum Mutat. 2012 Aug;33(8):1149-60. doi: 10.1002/humu.22086. Epub 2012 Apr 16. Review.

PubMed [citation]

PMID:: 22461308

The prevalence of CHD7 missense versus truncating mutations is higher in patients with Kallmann syndrome than in typical CHARGE patients.

Marcos S, Sarfati J, Leroy C, Fouveaut C, Parent P, Metz C, Wolczynski S, Gérard M, Bieth E, Kurtz F, Verier-Mine O, Perrin L, Archambeaud F, Cabrol S, Rodien P, Hove H, Prescott T, Lacombe D, Christin-Maitre S, Touraine P, Hieronimus S, Dewailly D, et al.

J Clin Endocrinol Metab. 2014 Oct;99(10):E2138-43. doi: 10.1210/jc.2014-2110. Epub 2014 Jul 31. Erratum in: J Clin Endocrinol Metab. 2015 Jan;100(1):317.

PubMed [citation]

PMID:: 25077900

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002137030.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with CHD7-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gln592Alafs*20) in the CHD7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CHD7 are known to be pathogenic (PMID: 22461308, 25077900).

#	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

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