CHD2 chromodomain helicase DNA binding protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHD2provided by HGNC
Official Full Name: chromodomain helicase DNA binding protein 2provided by HGNC
Primary source: HGNC:HGNC:1917
See related: Ensembl:ENSG00000173575 MIM:602119; AllianceGenome:HGNC:1917
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: EEOC; DEE94
Summary: The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in bone marrow (RPKM 26.2), thyroid (RPKM 13.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q26.1

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (92900324..93027996)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (90662587..90790268)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (93443554..93571226)

Chromosome 15 - NC_000015.10 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 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?

Clinical analysis of five CHD2 gene mutations in Chinese children with epilepsy.
Title: Clinical analysis of five CHD2 gene mutations in Chinese children with epilepsy.
Low-grade parental gonosomal mosaicism in CHD2 siblings with Smith-Magenis-like syndrome.
Title: Low-grade parental gonosomal mosaicism in CHD2 siblings with Smith-Magenis-like syndrome.
Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement.
Title: Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement.
Role of CircCHD2 in the pathogenesis of gestational diabetes mellitus by regulating autophagy via miR-33b-3p/ULK1 axis.
Title: Role of CircCHD2 in the pathogenesis of gestational diabetes mellitus by regulating autophagy via miR-33b-3p/ULK1 axis.
CircCHD2/miR-200b-3p/HLF Axis Promotes Liver Cirrhosis.
Title: CircCHD2/miR-200b-3p/HLF Axis Promotes Liver Cirrhosis.
Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2.
Title: Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2.
Novel Loss-of-Function Variants in CHD2 Cause Childhood-Onset Epileptic Encephalopathy in Chinese Patients.
Title: Novel Loss-of-Function Variants in CHD2 Cause Childhood-Onset Epileptic Encephalopathy in Chinese Patients.
CHD1 and SPOP synergistically protect prostate epithelial cells from DNA damage.
Title: CHD1 and SPOP synergistically protect prostate epithelial cells from DNA damage.
A regulatory role for CHD2 in myelopoiesis.
Title: A regulatory role for CHD2 in myelopoiesis.
CHD2-Related CNS Pathologies.
Title: CHD2-Related CNS Pathologies.

Submit: New GeneRIF Correction See all GeneRIFs (29)

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
Developmental and epileptic encephalopathy 94 MedGen: C3809278 OMIM: 615369 GeneReviews: CHD2-Related Neurodevelopmental Disorders	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2019-10-23) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2019-10-23) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH66633 (e-PCR)
- UniSTS:53254

RH11204 (e-PCR)
- UniSTS:86549

RH78806 (e-PCR)
- UniSTS:19225

RH44328 (e-PCR)
- UniSTS:29467

CHD2 (e-PCR)
- UniSTS:503082

SHGC-37648 (e-PCR)
- UniSTS:51253

HSCZYG012 (e-PCR)
- UniSTS:37195

1876 (e-PCR)
- UniSTS:24925

RH44878 (e-PCR)
- UniSTS:83057

D15S1494 (e-PCR)
- UniSTS:474496

RH93743 (e-PCR)
- UniSTS:88704

STS-N29696 (e-PCR)
- UniSTS:60548

WI-20731 (e-PCR)
- UniSTS:22951

A003M08 (e-PCR)
- UniSTS:17832

D15S1298 (e-PCR)
- UniSTS:41128

HSC2CD122 (e-PCR)
- UniSTS:31146

RH46033 (e-PCR)
- UniSTS:3267

RH80079 (e-PCR)
- UniSTS:84422

Clone Names

FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables forked DNA-dependent helicase activity	IEA Inferred from Electronic Annotation more info
enables four-way junction helicase activity	IEA Inferred from Electronic Annotation more info
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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded 3'-5' DNA helicase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA damage response	IEA Inferred from Electronic Annotation more info
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in hematopoietic stem cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in muscle organ development	ISS Inferred from Sequence or Structural Similarity more info
involved_in nucleosome organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 2

Names: ATP-dependent helicase CHD2; CHD-2

NP_001036037.1

EC 3.6.4.12

NP_001262.3

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_012826.2 RefSeqGene

Range

5004..132676

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1425

mRNA and Protein(s)

NM_001042572.3 → NP_001036037.1 chromodomain-helicase-DNA-binding protein 2 isoform 2

See identical proteins and their annotated locations for NP_001036037.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks multiple 3' exons and has an alternate 3' end, as compared to variant 1. The encoded isoform (2) has a much shorter and distinct C-terminus, as compared to isoform 1.

Source sequence(s)

BC007347, BU630151, CN277753

Consensus CDS

CCDS45356.1

UniProtKB/TrEMBL

Q8N677

Related

ENSP00000406581.2, ENST00000420239.7

Conserved Domains (3) summary

cd18661
Location:376 → 447

CD2_tandem_CHD1-2_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins

cd18666
Location:259 → 343

CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins

cl28899
Location:464 → 501

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
NM_001271.4 → NP_001262.3 chromodomain-helicase-DNA-binding protein 2 isoform 1

See identical proteins and their annotated locations for NP_001262.3

Status: REVIEWED

Description

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

Source sequence(s)

AA907775, AC013394, AF006514, CT003638, DB111282, DB121252

Consensus CDS

CCDS10374.2

UniProtKB/Swiss-Prot

C6G482, O14647, Q96IP5

Related

ENSP00000377747.4, ENST00000394196.9

Conserved Domains (8) summary

cd00024
Location:282 → 344

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:503 → 648

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:487 → 768

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:790 → 905

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:379 → 447

Chromo; Chromo (CHRromatin Organization MOdifier) domain

pfam08648
Location:1661 → 1749

DUF1777; Protein of unknown function (DUF1777)

pfam13907
Location:1471 → 1553

DUF4208; Domain of unknown function (DUF4208)

pfam17104
Location:1042 → 1165

DUF5102; Domain of unknown function (DUF5102)