CHD3

chromodomain helicase DNA binding protein 3, the group of Small nucleolar RNA protein coding host genes|PHD finger proteins|NuRD complex subunits

Basic information

Region (hg38): 17:7884796-7912760

Links

ENSG00000170004 ∙ NCBI:1107 ∙ OMIM:602120 ∙ HGNC:1918 ∙ Uniprot:Q12873 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Snijders Blok-Campeau syndrome (Strong), mode of inheritance: AD
• Snijders Blok-Campeau syndrome (Strong), mode of inheritance: AD
• Snijders Blok-Campeau syndrome (Definitive), mode of inheritance: AD
• Snijders Blok-Campeau syndrome (Definitive), mode of inheritance: AD
• Snijders Blok-Campeau syndrome (Limited), mode of inheritance: AR
• Snijders Blok-Campeau syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Snijders Blok-Campeau syndrome	AD	Cardiovascular	Among other features, the condition can include congenital cardiac anomalies, and awareness may enable early identification and management	Craniofacial; Cardiovascular; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic	29463886; 30397230; 32483341

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHD3 gene.

• Snijders Blok-Campeau syndrome (15 variants)
• not provided (9 variants)
• Inborn genetic diseases (5 variants)
• Intellectual disability (4 variants)
• CHD3-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHD3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	27	4	32
missense	8	47	290	28	1	374
nonsense	6	3	2			11
start loss						0
frameshift	8	6	3			17
inframe indel		2	7	4	3	16
splice donor/acceptor (+/-2bp)		3	2			5
splice region			9	7	1	17
non coding			3	2	3	8
Total	22	61	308	61	11

Variants in CHD3

This is a list of pathogenic ClinVar variants found in the CHD3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-7884837-G-A		Inborn genetic diseases	Uncertain significance (May 03, 2023)
17-7884848-G-A			Likely benign (Sep 01, 2024)
17-7884851-G-A		Snijders Blok-Campeau syndrome	Uncertain significance (Sep 22, 2024)
17-7884872-A-C		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
17-7884876-G-A			Uncertain significance (May 01, 2020)
17-7884889-GCGA-G			Uncertain significance (Dec 15, 2022)
17-7884893-CGAG-C			Benign (Aug 01, 2022)
17-7884894-G-A			Uncertain significance (Aug 02, 2019)
17-7884913-T-A			Uncertain significance (Nov 14, 2023)
17-7884927-G-A			Uncertain significance (May 23, 2023)
17-7884927-G-C		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
17-7884933-G-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
17-7884935-T-G		Inborn genetic diseases	Uncertain significance (Dec 10, 2024)
17-7884942-G-A			Uncertain significance (Jul 10, 2020)
17-7884945-G-T			Uncertain significance (Mar 13, 2023)
17-7884957-G-C		Inborn genetic diseases	Uncertain significance (Sep 19, 2024)
17-7884970-G-C			Uncertain significance (Apr 10, 2024)
17-7884982-A-G			Uncertain significance (Dec 07, 2022)
17-7884993-G-C			Uncertain significance (Nov 03, 2021)
17-7884996-C-T			Uncertain significance (Aug 05, 2024)
17-7884999-C-T			Uncertain significance (Jul 01, 2024)
17-7885005-C-T		Inborn genetic diseases	Uncertain significance (Jul 31, 2024)
17-7885011-G-A			Uncertain significance (Dec 01, 2022)
17-7885021-T-G			Uncertain significance (Aug 01, 2019)
17-7885025-CCCG-C		Inborn genetic diseases	Benign/Likely benign (May 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHD3	protein_coding	protein_coding	ENST00000380358	40	27955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.51e-12	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	6.15	591	1.19e+3	0.498	0.0000735	13412
Missense in Polyphen		49	140.02	0.34996		1544
Synonymous	0.0403	467	468	0.998	0.0000295	3981
Loss of Function	9.10	10	115	0.0866	0.00000698	1267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000119
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000111	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. {ECO:0000269|PubMed:17626165, ECO:0000269|PubMed:9804427}.
• Pathway: ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);Generic Transcription Pathway;SUMOylation of chromatin organization proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;HDACs deacetylate histones;Metabolism of proteins;RNA Polymerase I Promoter Clearance;RNA Polymerase II Transcription;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;SUMOylation;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Intracellular signaling by second messengers;Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.0137
• rvis_EVS: -2.48
• rvis_percentile_EVS: 0.97

Haploinsufficiency Scores

• pHI: 0.813
• hipred: Y
• hipred_score: 0.765
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Chd3

Zebrafish Information Network

• Gene name: chd3
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: chromatin assembly or disassembly;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;spindle organization;centrosome cycle;histone deacetylation;DNA duplex unwinding
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;centrosome;microtubule organizing center;NuRD complex
• Molecular function: DNA binding;RNA binding;ATP-dependent DNA helicase activity;helicase activity;histone deacetylase activity;protein binding;ATP binding;zinc ion binding