CHD6

protein-coding

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

Gene summary

This gene encodes a member of the SNF2/RAD54 helicase protein family. The encoded protein contains two chromodomains, a helicase domain, and an ATPase domain. Several multi-subunit protein complexes remodel chromatin to allow patterns of cell type-specific gene expression, and the encoded protein is thought to be a core member of one or more of these chromatin remodeling complexes. The encoded protein may function as a transcriptional repressor and is involved in the cellular repression of influenza virus replication. [provided by RefSeq, Jul 2013]

MANE transcript

NM_032221.5

Inheritance

—

ClinVar variants

U:296B:38

Top phenotype

CHD6-related disorder

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr20:41,402,083-41,618,384

External References & Databases

Ensembl (ENSG00000124177)

Transcript & Mutation Effects

hg38 • Region Span ~216.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHD6 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 272

not providedTotal: 40

CHD6-related disorderTotal: 2

CHD6-related neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032221.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	13 clinvar	6 clinvar	25
missense			271 clinvar	15 clinvar	4 clinvar	290
nonsense			6 clinvar			6
start loss						0
frameshift			4 clinvar			4
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	296	28	10	334

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032221.5	RefSeq	NP_115597.3	36	MANE Select
ENST00000373233.8	Ensembl	ENSP00000362330.3	36	MANE Select
ENST00000373222.3	Ensembl	ENSP00000362319.3	6	Standard
ENST00000373222.4	Ensembl	ENSP00000362319.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chromatin organization
viral process
positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress

Molecular Function

transcription cofactor binding
DNA binding
helicase activity
ATP binding
DNA-dependent ATPase activity

Cellular Component

nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373233
Coding exons: 36
Length: 216393
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125748
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.00	1060	1.50e+3	0.709	0.0000842	17928
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.000062	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.950

Gene Damage Prediction

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