NM_017780.4(CHD7):c.1791GAA[2] (p.Lys602del) AND CHARGE syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 17, 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:: RCV000689706.5

Allele description [Variation Report for NM_017780.4(CHD7):c.1791GAA[2] (p.Lys602del)]

NM_017780.4(CHD7):c.1791GAA[2] (p.Lys602del)

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:

Microsatellite

Cytogenetic location:

8q12.2

Genomic location:

Preferred name:

NM_017780.4(CHD7):c.1791GAA[2] (p.Lys602del)

HGVS:

NC_000008.11:g.60781125GAA[2]
NG_007009.1:g.107346GAA[2]
NM_001316690.1:c.1716+73AAG[2]
NM_017780.4:c.1791GAA[2]MANE SELECT
NP_060250.2:p.Lys602del
LRG_176:g.107346GAA[2]
NC_000008.10:g.61693682_61693684del
NC_000008.10:g.61693684GAA[2]
NM_017780.3:c.1797_1799delGAA

Protein change:

K602del

Links:

dbSNP: rs757119372

NCBI 1000 Genomes Browser:

rs757119372

Molecular consequence:

NM_017780.4:c.1791GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001316690.1:c.1716+73AAG[2] - 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

Recent activity

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hypothetical protein EQP60_14560 [Listeria monocytogenes]
hypothetical protein EQP60_14560 [Listeria monocytogenes]
gi|1560718388|gnl|PRJNA515219|EQP60 0|gb|QAS38023.1|

Protein
thiol reductant ABC exporter subunit CydC [Listeria monocytogenes]
thiol reductant ABC exporter subunit CydC [Listeria monocytogenes]
gi|1560718385|gnl|PRJNA515219|EQP60 5|gb|QAS38020.1|

Protein
Mus musculus rhomboid family 1 (Drosophila), mRNA (cDNA clone IMAGE:5029198), pa...
Mus musculus rhomboid family 1 (Drosophila), mRNA (cDNA clone IMAGE:5029198), partial cds
gi|19483908|gb|BC023469.1|

Nucleotide
Homologene neighbors for GEO Profiles (Select 103998865) (0)
GEO Profiles
Homologene neighbors for GEO Profiles (Select 119861549) (0)
GEO Profiles

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000817370	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 17, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000817370

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 17, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000817370.4

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

Description

Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 569146). This variant has not been reported in the literature in individuals affected with CHD7-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.005%). This variant, c.1797_1799del, results in the deletion of 1 amino acid(s) of the CHD7 protein (p.Lys602del), but otherwise preserves the integrity of the reading frame. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

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