CHD9

chromodomain helicase DNA binding protein 9

Basic information

Region (hg38): 16:53054991-53329150

Links

ENSG00000177200 ∙ NCBI:80205 ∙ OMIM:616936 ∙ HGNC:25701 ∙ Uniprot:Q3L8U1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHD9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHD9 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				4		4
missense			121	2	1	124
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	122	6	1

Variants in CHD9

This is a list of pathogenic ClinVar variants found in the CHD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-53156102-A-T		not specified	Uncertain significance (Oct 03, 2022)
16-53156115-T-C		not specified	Uncertain significance (Jun 24, 2022)
16-53156184-C-T		not specified	Uncertain significance (Dec 28, 2023)
16-53156298-A-C		not specified	Uncertain significance (Sep 30, 2024)
16-53156348-G-A		not specified	Uncertain significance (May 04, 2022)
16-53156420-C-T		not specified	Uncertain significance (Jun 09, 2022)
16-53156424-A-G		not specified	Uncertain significance (Mar 04, 2024)
16-53156453-A-C		not specified	Uncertain significance (Dec 28, 2023)
16-53156531-C-T		not specified	Uncertain significance (Mar 29, 2022)
16-53156537-A-G		not specified	Uncertain significance (Mar 29, 2024)
16-53156589-C-T		not specified	Uncertain significance (Mar 07, 2023)
16-53156600-C-A		not specified	Uncertain significance (Apr 27, 2022)
16-53156621-C-T		not specified	Uncertain significance (Apr 29, 2024)
16-53156625-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-53156747-T-C		not specified	Uncertain significance (Jun 05, 2023)
16-53156773-G-A		not specified	Uncertain significance (Jun 05, 2024)
16-53156790-C-T		not specified	Uncertain significance (Feb 05, 2024)
16-53156795-A-G		not specified	Uncertain significance (Aug 09, 2021)
16-53156894-C-G		not specified	Uncertain significance (Aug 29, 2024)
16-53156960-G-T		not specified	Uncertain significance (Oct 10, 2023)
16-53156969-G-C		not specified	Uncertain significance (Jul 31, 2024)
16-53156984-A-G		not specified	Uncertain significance (Sep 29, 2023)
16-53157069-A-G		not specified	Uncertain significance (May 26, 2023)
16-53157122-C-A		not specified	Uncertain significance (Sep 20, 2024)
16-53157138-G-A		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHD9	protein_coding	protein_coding	ENST00000566029	38	274118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.66e-12	124630	0	23	124653	0.0000923

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.77	1050	1.45e+3	0.722	0.0000742	18846
Missense in Polyphen		318	556.05	0.57189		7315
Synonymous	0.353	488	498	0.980	0.0000251	5455
Loss of Function	9.62	15	136	0.110	0.00000769	1710

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000147	0.000142
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. Proposed to be a ATP-dependent chromatin remodeling protein. Has DNA-dependent ATPase activity and binds to A/T-rich DNA. Associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis (By similarity). {ECO:0000250, ECO:0000269|PubMed:16095617, ECO:0000269|PubMed:16554032}.
• Pathway: Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;Metabolism (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.0877
• rvis_EVS: -2.18
• rvis_percentile_EVS: 1.4

Haploinsufficiency Scores

• pHI: 0.859
• hipred: Y
• hipred_score: 0.648
• ghis: 0.674

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.510

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chd9
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: chromatin organization;regulation of lipid metabolic process
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: DNA binding;helicase activity;ATP binding