CHD8 chromodomain helicase DNA binding protein 8 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHD8provided by HGNC
Official Full Name: chromodomain helicase DNA binding protein 8provided by HGNC
Primary source: HGNC:HGNC:20153
See related: Ensembl:ENSG00000100888 MIM:610528; AllianceGenome:HGNC:20153
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: IDDAM; AUTS18; HELSNF1
Summary: This gene encodes a member of the chromodomain-helicase-DNA binding protein family, which is characterized by a SNF2-like domain and two chromatin organization modifier domains. The encoded protein also contains brahma and kismet domains, which are common to the subfamily of chromodomain-helicase-DNA binding proteins to which this protein belongs. This gene has been shown to function in several processes that include transcriptional regulation, epigenetic remodeling, promotion of cell proliferation, and regulation of RNA synthesis. Allelic variants of this gene are associated with autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2016]
Expression: Ubiquitous expression in thyroid (RPKM 9.5), brain (RPKM 8.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q11.2

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (21385199..21456123, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (15582676..15653513, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (21853358..21924282, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Shared and divergent mental health characteristics of ADNP-, CHD8- and DYRK1A-related neurodevelopmental conditions.
Title: Shared and divergent mental health characteristics of ADNP-, CHD8- and DYRK1A-related neurodevelopmental conditions.
Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction.
Title: Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction.
CHD8 suppression impacts on histone H3 lysine 36 trimethylation and alters RNA alternative splicing.
Title: CHD8 suppression impacts on histone H3 lysine 36 trimethylation and alters RNA alternative splicing.
The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1.
Title: The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1.
Autism-associated CHD8 keeps proliferation of human neural progenitors in check by lengthening the G1 phase of the cell cycle.
Title: Autism-associated CHD8 keeps proliferation of human neural progenitors in check by lengthening the G1 phase of the cell cycle.
The phenotypic spectrum and genotype-phenotype correlations in 106 patients with variants in major autism gene CHD8.
Title: The phenotypic spectrum and genotype-phenotype correlations in 106 patients with variants in major autism gene CHD8.
Childhood-onset progressive dystonia associated with pathogenic truncating variants in CHD8.
Title: Childhood-onset progressive dystonia associated with pathogenic truncating variants in CHD8.
CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories.
Title: CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories.
The Mechanisms of CHD8 in Neurodevelopment and Autism Spectrum Disorders.
Title: The Mechanisms of CHD8 in Neurodevelopment and Autism Spectrum Disorders.
Heterozygous nonsense variant of CHD8 in a patient with forme-fruste Marfan syndrome and intellectual disability.
Title: Heterozygous nonsense variant of CHD8 in a patient with forme-fruste Marfan syndrome and intellectual disability.

Submit: New GeneRIF Correction See all GeneRIFs (47)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual developmental disorder with autism and macrocephaly MedGen: C3554373 OMIM: 615032 GeneReviews: CHD8-Related Neurodevelopmental Disorder with Overgrowth	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2018-04-25) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2018-04-25) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-20203 (e-PCR)
- UniSTS:29445

BE589327 (e-PCR)
- UniSTS:519197

D14S1321 (e-PCR)
- UniSTS:65859

G36016 (e-PCR)
- UniSTS:24975

WI-14045 (e-PCR)
- UniSTS:39614

RH119001 (e-PCR)
- UniSTS:138969

G20455 (e-PCR)
- UniSTS:12256

A005R45 (e-PCR)
- UniSTS:12257

A004V16 (e-PCR)
- UniSTS:61411

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent chromatin remodeler activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent chromatin remodeler activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables beta-catenin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables p53 binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in digestive tract development	IBA Inferred from Biological aspect of Ancestor more info
involved_in digestive tract development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of fibroblast apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase III	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in prepulse inhibition	IEA Inferred from Electronic Annotation more info
involved_in social behavior	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of MLL1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of MLL1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 8

Names: ATP-dependent helicase CHD8; axis duplication inhibitor; duplin; helicase with SNF2 domain 1

NP_001164100.1

EC 3.6.4.12

NP_065971.2

EC 3.6.4.12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_021249.2 RefSeqGene

Range

5000..75924

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001170629.2 → NP_001164100.1 chromodomain-helicase-DNA-binding protein 8 isoform 1

See identical proteins and their annotated locations for NP_001164100.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB046784, AK122910, AL161747, BC036920

Consensus CDS

CCDS53885.1

UniProtKB/Swiss-Prot

Q4G0D8, Q68DQ0, Q6DKH9, Q6P440, Q6ZNL7, Q8N3Z9, Q8NCY4, Q8TBR9, Q96F26, Q9HCK8

Related

ENSP00000495240.1, ENST00000646647.2

Conserved Domains (6) summary

smart00592
Location:2310 → 2354

BRK; domain in transcription and CHROMO domain helicases

cd00024
Location:644 → 704

CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...

cd00046
Location:830 → 979

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00176
Location:814 → 1101

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1133 → 1247

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:725 → 781

Chromo; Chromo (CHRromatin Organization MOdifier) domain
NM_020920.4 → NP_065971.2 chromodomain-helicase-DNA-binding protein 8 isoform 2

See identical proteins and their annotated locations for NP_065971.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and has a distinct 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AB046784, AK122910, AL834524, BC036920, CN290520

Consensus CDS

CCDS45081.1

UniProtKB/Swiss-Prot

Q9HCK8

Related

ENSP00000406288.3, ENST00000430710.8

Conserved Domains (6) summary

smart00592
Location:2031 → 2075

BRK; domain in transcription and CHROMO domain helicases

cd00024
Location:365 → 425

CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...

cd00046
Location:551 → 700

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00176
Location:535 → 822

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:854 → 968

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:446 → 502

Chromo; Chromo (CHRromatin Organization MOdifier) domain