NM_017780.4(CHD7):c.8550T>G (p.Asn2850Lys) AND CHARGE syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 12, 2022
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:: RCV002941999.2

Allele description

NM_017780.4(CHD7):c.8550T>G (p.Asn2850Lys)

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.8550T>G (p.Asn2850Lys)

HGVS:

NC_000008.11:g.60865489T>G
NG_007009.1:g.191710T>G
NM_001316690.1:c.2403T>G
NM_017780.4:c.8550T>GMANE SELECT
NP_001303619.1:p.Asn801Lys
NP_060250.2:p.Asn2850Lys
NP_060250.2:p.Asn2850Lys
LRG_176t1:c.8550T>G
LRG_176:g.191710T>G
LRG_176p1:p.Asn2850Lys
NC_000008.10:g.61778048T>G
NM_017780.2:c.8550T>G

Protein change:

N2850K

Molecular consequence:

NM_001316690.1:c.2403T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_017780.4:c.8550T>G - missense variant - [Sequence Ontology: SO:0001583]

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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Homo sapiens acid phosphatase 5, tartrate resistant, mRNA (cDNA clone MGC:117378...
Homo sapiens acid phosphatase 5, tartrate resistant, mRNA (cDNA clone MGC:117378 IMAGE:5181082), complete cds
gi|83405785|gb|BC111014.1|

Nucleotide
Homo sapiens prostrate kallikrein 2 (KLK2) mRNA, alternatively spliced, complete...
Homo sapiens prostrate kallikrein 2 (KLK2) mRNA, alternatively spliced, complete cds
gi|6425043|gb|AF188745.1|

Nucleotide
Homo sapiens fructose-1,6-bisphosphatase 2, mRNA (cDNA clone MGC:151086 IMAGE:40...
Homo sapiens fructose-1,6-bisphosphatase 2, mRNA (cDNA clone MGC:151086 IMAGE:40126028), complete cds
gi|109658925|gb|BC117477.1|

Nucleotide
Homo sapiens family with sequence similarity 19 (chemokine (C-C motif)-like), me...
Homo sapiens family with sequence similarity 19 (chemokine (C-C motif)-like), member A3, mRNA (cDNA clone MGC:151088 IMAGE:40126030), complete cds
gi|109658927|gb|BC117479.1|

Nucleotide
xaa-Pro dipeptidase isoform 1 [Mus musculus]
xaa-Pro dipeptidase isoform 1 [Mus musculus]
gi|170650724|ref|NP_032846.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003268411	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 12, 2022)	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

SCV003268411

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 12, 2022)

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 Invitae, SCV003268411.2

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

Description

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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CHD7 protein function. This variant has not been reported in the literature in individuals affected with CHD7-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 2850 of the CHD7 protein (p.Asn2850Lys).

#	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: Jun 2, 2024

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