VCV003376256.1 - ClinVar

NM_001273.5(CHD4):c.1726C>T (p.Arg576Trp)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001273.5(CHD4):c.1726C>T (p.Arg576Trp)

Variation ID: 3376256 Accession: VCV003376256.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 12p13.31 12: 6598060 (GRCh38) [ NCBI UCSC ] 12: 6707226 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 19, 2024	Nov 17, 2024	Aug 24, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001273.5:c.1726C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001264.2:p.Arg576Trp	missense
NM_001297553.2:c.1705C>T	NP_001284482.1:p.Arg569Trp	missense
NM_001363606.2:c.1687C>T	NP_001350535.1:p.Arg563Trp	missense
NC_000012.12:g.6598060G>A
NC_000012.11:g.6707226G>A
NG_052823.1:g.14380C>T

... more HGVS ... less HGVS

Protein change

R563W, R569W, R576W

Other names

Canonical SPDI

NC_000012.12:6598059:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
CHD4		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	557	606

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Sifrim-Hitz-Weiss syndrome	Likely pathogenic (1)	criteria provided, single submitter	Aug 24, 2022	RCV004784992.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely Pathogenic (Aug 24, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Sifrim-Hitz-Weiss syndrome (Autosomal dominant inheritance) Affected status: yes Allele origin: germline	Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center Accession: SCV005397341.1 First in ClinVar: Nov 17, 2024 Last updated: Nov 17, 2024	Publications: PubMed (2) PubMed: 22575888‚ 21743468 Comment: This sequence variant is a single nucleotide substitution (C>T) at coding position 1726 of the CHD4 gene that results in an arginine to tryptophan amino … (more) This sequence variant is a single nucleotide substitution (C>T) at coding position 1726 of the CHD4 gene that results in an arginine to tryptophan amino acid change at residue 576 of the CHD4 protein. This is a de novo variant that has not been previously reported in databases of clinically annotated variants but has been observed in the literature in an individual with a neuropsychiatric disorder (PMID: 21743468). This variant is absent from control population datasets (gnomAD database 0 of ~250,000 alleles). Multiple bioinformatic tools predict that this variant would be damaging and the Arg576 residue is highly conserved across the vertebrate species examined. This variant is found within the chromo 1 domain of the CHD4 protein which is important for its ATPase and nucleosome remodeling activity (PMID: 22575888). Functiol studies testing the effect of this variant on protein structure or activity have not been performed, to our knowledge. Given the currently available evidence, we consider this variant to be likely pathogenic. ACMG Criteria: PM2, PP3, PS2 (less)

Comment:

This sequence variant is a single nucleotide substitution (C>T) at coding position 1726 of the CHD4 gene that results in an arginine to tryptophan amino acid change at residue 576 of the CHD4 protein. This is a de novo variant that has not been previously reported in databases of clinically annotated variants but has been observed in the literature in an individual with a neuropsychiatric disorder (PMID: 21743468). This variant is absent from control population datasets (gnomAD database 0 of ~250,000 alleles). Multiple bioinformatic tools predict that this variant would be damaging and the Arg576 residue is highly conserved across the vertebrate species examined. This variant is found within the chromo 1 domain of the CHD4 protein which is important for its ATPase and nucleosome remodeling activity (PMID: 22575888). Functiol studies testing the effect of this variant on protein structure or activity have not been performed, to our knowledge. Given the currently available evidence, we consider this variant to be likely pathogenic. ACMG Criteria: PM2, PP3, PS2

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
The PHD and chromo domains regulate the ATPase activity of the human chromatin remodeler CHD4.	Watson AA	Journal of molecular biology	2012	PMID: 22575888
Increased exonic de novo mutation rate in individuals with schizophrenia.	Girard SL	Nature genetics	2011	PMID: 21743468

Text-mined citations for this variant ...

Record last updated Nov 19, 2024

ClinVar Genomic variation as it relates to human health

NM_001273.5(CHD4):c.1726C>T (p.Arg576Trp)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...