CHD6

chromodomain helicase DNA binding protein 6, the group of Myb/SANT domain containing

Basic information

Region (hg38): 20:41402083-41618384

Links

ENSG00000124177 ∙ NCBI:84181 ∙ OMIM:616114 ∙ HGNC:19057 ∙ Uniprot:Q8TD26 ∙ 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 CHD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHD6 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	8	7	16
missense			92	6	6	104
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					1	1
Total	0	0	93	14	14

Variants in CHD6

This is a list of pathogenic ClinVar variants found in the CHD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-41404604-C-A		not specified	Uncertain significance (Aug 09, 2021)
20-41404625-C-T		not specified	Uncertain significance (Sep 16, 2022)
20-41404744-T-C		not specified	Uncertain significance (Dec 16, 2023)
20-41404765-T-G		not specified	Uncertain significance (Apr 12, 2023)
20-41404806-C-T			Benign (Jun 10, 2018)
20-41404844-C-T		not specified	Uncertain significance (Jan 10, 2023)
20-41404846-A-G		not specified	Uncertain significance (Aug 04, 2021)
20-41404853-G-C		not specified	Uncertain significance (Dec 22, 2023)
20-41404863-C-T		not specified	Uncertain significance (Mar 18, 2024)
20-41405085-C-T			Likely benign (Mar 29, 2018)
20-41405149-A-G		not specified	Uncertain significance (Feb 28, 2023)
20-41405177-G-C		not specified	Uncertain significance (Mar 18, 2024)
20-41405337-G-T		not specified	Uncertain significance (Dec 03, 2021)
20-41405381-G-A		not specified	Uncertain significance (Jan 19, 2024)
20-41405401-C-T		not specified	Uncertain significance (Nov 15, 2021)
20-41405415-C-A		not specified	Uncertain significance (Nov 21, 2022)
20-41405415-C-G		not specified	Uncertain significance (Oct 27, 2021)
20-41405416-C-G		not specified	Uncertain significance (Jan 27, 2022)
20-41405464-T-C		not specified	Uncertain significance (Aug 22, 2023)
20-41412148-A-G		not specified	Uncertain significance (Sep 17, 2021)
20-41412185-C-G			Benign (Dec 31, 2019)
20-41412230-G-A		not specified	Benign (May 05, 2015)
20-41413370-A-C		not specified	Uncertain significance (Oct 26, 2022)
20-41413491-C-T			Benign (Oct 11, 2018)
20-41415178-A-G			Likely benign (Jan 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHD6	protein_coding	protein_coding	ENST00000373233	36	216393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.41e-18	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.00	1060	1.50e+3	0.709	0.0000842	17928
Missense in Polyphen		257	563.18	0.45634		6536
Synonymous	0.843	546	572	0.955	0.0000336	5193
Loss of Function	10.1	4	126	0.0317	0.00000701	1500

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000451	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA-dependent ATPase that plays a role in chromatin remodeling. Regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin (PubMed:28533432). Activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2. {ECO:0000269|PubMed:16314513, ECO:0000269|PubMed:28533432}.

Recessive Scores

• pRec: 0.0995

Intolerance Scores

• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.91

Haploinsufficiency Scores

• pHI: 0.822
• hipred: Y
• hipred_score: 0.673
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chd6
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: chromatin organization;viral process;positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress
• Cellular component: nucleoplasm
• Molecular function: transcription cofactor binding;DNA binding;helicase activity;ATP binding;DNA-dependent ATPase activity