CHD5 chromodomain helicase DNA binding protein 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHD5provided by HGNC
Official Full Name: chromodomain helicase DNA binding protein 5provided by HGNC
Primary source: HGNC:HGNC:16816
See related: Ensembl:ENSG00000116254 MIM:610771; AllianceGenome:HGNC:16816
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CHD-5; PMNDS
Summary: This gene encodes a member of the chromodomain helicase DNA-binding protein family. Members of this family are characterized by a chromodomain, a helicase ATP-binding domain and an additional functional domain. This gene encodes a neuron-specific protein that may function in chromatin remodeling and gene transcription. This gene is a potential tumor suppressor gene that may play a role in the development of neuroblastoma. [provided by RefSeq, Feb 2012]
Expression: Biased expression in brain (RPKM 14.5), testis (RPKM 9.9) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.31

Exon count:: 42

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (6101787..6180321, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (5627473..5705967, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (6161847..6240381, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

CHD5 gene variant predicts leptomeningeal metastasis after surgical resection of brain metastases of breast cancer.
Title: CHD5 gene variant predicts leptomeningeal metastasis after surgical resection of brain metastases of breast cancer.
CHD5 gene (rs9434741) might be a genetic risk factor for infertility in non-obstructive azoospermia and severe oligozoospermia.
Title: CHD5 gene (rs9434741) might be a genetic risk factor for infertility in non-obstructive azoospermia and severe oligozoospermia.
Pan-Cancer Analysis Identifies CHD5 as a Potential Biomarker for Glioma.
Title: Pan-Cancer Analysis Identifies CHD5 as a Potential Biomarker for Glioma.
mRNA expression and epigenetic-based role of chromodomain helicase DNA-binding 5 in hepatocellular carcinoma.
Title: mRNA expression and epigenetic-based role of chromodomain helicase DNA-binding 5 in hepatocellular carcinoma.
Missense and truncating variants in CHD5 in a dominant neurodevelopmental disorder with intellectual disability, behavioral disturbances, and epilepsy.
Title: Missense and truncating variants in CHD5 in a dominant neurodevelopmental disorder with intellectual disability, behavioral disturbances, and epilepsy.
Chromodomain Helicase DNA-Binding Protein 5 Inhibits Renal Cell Carcinoma Tumorigenesis by Activation of the p53 and RB Pathways.
Title: Chromodomain Helicase DNA-Binding Protein 5 Inhibits Renal Cell Carcinoma Tumorigenesis by Activation of the p53 and RB Pathways.
SLC16A1-AS1 enhances radiosensitivity and represses cell proliferation and invasion by regulating the miR-301b-3p/CHD5 axis in hepatocellular carcinoma.
Title: SLC16A1-AS1 enhances radiosensitivity and represses cell proliferation and invasion by regulating the miR-301b-3p/CHD5 axis in hepatocellular carcinoma.
Our results suggest that the rare CHD5 gene haplotype and alcohol intake contribute to the risk of hepatocellular carcinoma
Title: A rare CHD5 haplotype and its interactions with environmental factors predicting hepatocellular carcinoma risk.
CHD5 was identified as a direct target of miR-454. CHD5 was downregulated in GC tissues/cell lines and the expresssion of CHD5 inversely correlated with the level of miR-454 in GC tissues. Taken together, these observations indicate that HDAC3 is associated with GC cell growth via the miR-454-mediated targeting of CHD5.
Title: Histone deacetylase 3 is associated with gastric cancer cell growth via the miR-454-mediated targeting of CHD5.
Data show that chromodomain helicase DNA binding protein 5 (CHD5) acted as a functional tumor suppressor and was frequently silenced by promoter CpG methylation in renal cell carcinoma (RCC).
Title: The epigenetic modifier CHD5 functions as a novel tumor suppressor for renal cell carcinoma and is predominantly inactivated by promoter CpG methylation.

Submit: New GeneRIF Correction See all GeneRIFs (41)

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
Parenti-mignot neurodevelopmental syndrome MedGen: C5676984 OMIM: 619873 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity Not yet evaluated (Last evaluated 2022-09-27) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2022-09-27) 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

SHGC-108153 (e-PCR)
- UniSTS:173873

G29319 (e-PCR)
- UniSTS:64121

CHD5_8020 (e-PCR)
- UniSTS:467602

SHGC-74144 (e-PCR)
- UniSTS:71077

RH80639 (e-PCR)
- UniSTS:86489

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 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 H3K27me3 modified histone binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cerebral cortex neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
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 negative regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of signal transduction by p53 class mediator	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sperm DNA condensation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NuRD complex	ISS Inferred from Sequence or Structural Similarity more info
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
part_of heterochromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	HDA more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay 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

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 5

Names: ATP-dependent helicase CHD5

NP_056372.1

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.

mRNA and Protein(s)

NM_015557.3 → NP_056372.1 chromodomain-helicase-DNA-binding protein 5

See identical proteins and their annotated locations for NP_056372.1

Status: VALIDATED

Source sequence(s)

AF425231, AL031847, AL035406, AW005809

Consensus CDS

CCDS57.1

UniProtKB/Swiss-Prot

O75032, Q5TG89, Q7LGH2, Q8TDI0, Q9UFR9

Related

ENSP00000262450.3, ENST00000262450.8

Conserved Domains (10) summary

smart00298
Location:592 → 625

CHROMO; Chromatin organization modifier domain

cd00046
Location:720 → 878

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.

cd15531
Location:345 → 387

PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

cd15532
Location:418 → 460

PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

pfam00176
Location:703 → 999

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1023 → 1138

Helicase_C; Helicase conserved C-terminal domain

pfam06461
Location:1388 → 1529

DUF1086; Domain of Unknown Function (DUF1086)

pfam06465
Location:1298 → 1358

DUF1087; Domain of Unknown Function (DUF1087)

pfam08073
Location:150 → 199

CHDNT; CHDNT (NUC034) domain

pfam08074
Location:1732 → 1903

CHDCT2; CHDCT2 (NUC038) domain