NC_000008.10:g.(?_61720756)_(61720851_?)del AND CHARGE syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 6, 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:: RCV004583251.2

Allele description [Variation Report for NC_000008.10:g.(?_61720756)_(61720851_?)del]

NC_000008.10:g.(?_61720756)_(61720851_?)del

Gene:: CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 8q12.2
Genomic location:: Chr8: 61720756 - 61720851 (on Assembly GRCh37)
Preferred name:: NC_000008.10:g.(?_61720756)_(61720851_?)del
HGVS:: NC_000008.10:g.(?_61720756)_(61720851_?)del
This HGVS expression did not pass validation

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

Recent activity

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cytochrome oxidase subunit I, partial (mitochondrion) [Gymnoris xanthocollis]
cytochrome oxidase subunit I, partial (mitochondrion) [Gymnoris xanthocollis]
gi|511782877|gb|AGN94991.1|

Protein
ornithine decarboxylase, partial [Gymnoris superciliaris]
ornithine decarboxylase, partial [Gymnoris superciliaris]
gi|629678428|gb|AHY87494.1|

Protein
glyceraldehyde-3-phosphodehydrogenase, partial [Gymnoris superciliaris]
glyceraldehyde-3-phosphodehydrogenase, partial [Gymnoris superciliaris]
gi|629676940|gb|AHY86752.1|

Protein
glyceraldehyde-3-phosphate dehydrogenase, partial [Pytilia melba]
glyceraldehyde-3-phosphate dehydrogenase, partial [Pytilia melba]
gi|1818983292|gb|QII14976.1|

Protein
Homo sapiens erythrocyte membrane protein band 4.1 like 1 (EPB41L1), transcript ...
Homo sapiens erythrocyte membrane protein band 4.1 like 1 (EPB41L1), transcript variant 16, mRNA
gi|2580429234|ref|NM_001424383.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005062861	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 6, 2023)	unknown	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

SCV005062861

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 6, 2023)

unknown

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	unknown	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, SCV005062861.1

#	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 affected with CHD7-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 7 of the CHD7 gene. This deletion is out-of-frame, and is expected to create a premature termination codon and 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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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