ERCC6 ERCC excision repair 6, chromatin remodeling factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: ERCC6provided by HGNC
Official Full Name: ERCC excision repair 6, chromatin remodeling factorprovided by HGNC
Primary source: HGNC:HGNC:3438
See related: Ensembl:ENSG00000225830 MIM:609413
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: CSB; CKN2; COFS; ARMD5; COFS1; POF11; RAD26; UVSS1; CSB-PGBD3
Summary: This gene encodes a DNA-binding protein that is important in transcription-coupled excision repair. The encoded protein has ATP-stimulated ATPase activity, interacts with several transcription and excision repair proteins, and may promote complex formation at DNA repair sites. Mutations in this gene are associated with Cockayne syndrome type B and cerebrooculofacioskeletal syndrome 1. Alternative splicing occurs between a splice site from exon 5 of this gene to the 3' splice site upstream of the open reading frame (ORF) of the adjacent gene, piggyback-derived-3 (GeneID:267004), which activates the alternative polyadenylation site downstream of the piggyback-derived-3 ORF. The resulting transcripts encode a fusion protein that shares sequence with the product of each individual gene. [provided by RefSeq, Mar 2016]
Expression: Ubiquitous expression in thyroid (RPKM 2.7), skin (RPKM 2.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q11.23

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
109.20211119	current	GRCh38.p13 (GCF_000001405.39)	10	NC_000010.11 (49434881..49539538, complement)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (50642927..50747584, complement)

Chromosome 10 - NC_000010.11 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?

Neuroblastoma Cells Depend on CSB for Faithful Execution of Cytokinesis and Survival.
Title: Neuroblastoma Cells Depend on CSB for Faithful Execution of Cytokinesis and Survival.
Cockayne Syndrome-Associated CSA and CSB Mutations Impair Ribosome Biogenesis, Ribosomal Protein Stability, and Global Protein Folding.
Title: Cockayne Syndrome-Associated CSA and CSB Mutations Impair Ribosome Biogenesis, Ribosomal Protein Stability, and Global Protein Folding.
Cockayne syndrome proteins CSA and CSB maintain mitochondrial homeostasis through NAD(+) signaling.
Title: Cockayne syndrome proteins CSA and CSB maintain mitochondrial homeostasis through NAD<sup>+</sup> signaling.
A role for the Cockayne Syndrome B (CSB)-Elongin ubiquitin ligase complex in signal-dependent RNA polymerase II transcription.
Title: A role for the Cockayne Syndrome B (CSB)-Elongin ubiquitin ligase complex in signal-dependent RNA polymerase II transcription.
LEO1 is a partner for Cockayne syndrome protein B (CSB) in response to transcription-blocking DNA damage.
Title: LEO1 is a partner for Cockayne syndrome protein B (CSB) in response to transcription-blocking DNA damage.
Clinical and Mutation Spectra of Cockayne Syndrome in India.
Title: Clinical and Mutation Spectra of Cockayne Syndrome in India.
The Winged Helix Domain of CSB Regulates RNAPII Occupancy at Promoter Proximal Pause Sites.
Title: The Winged Helix Domain of CSB Regulates RNAPII Occupancy at Promoter Proximal Pause Sites.
Cockayne Syndrome Group B (CSB): The Regulatory Framework Governing the Multifunctional Protein and Its Plausible Role in Cancer.
Title: Cockayne Syndrome Group B (CSB): The Regulatory Framework Governing the Multifunctional Protein and Its Plausible Role in Cancer.
Integrative genomic analysis implicates ERCC6 and its interaction with ERCC8 in susceptibility to breast cancer.
Title: Integrative genomic analysis implicates ERCC6 and its interaction with ERCC8 in susceptibility to breast cancer.
Current and emerging roles of Cockayne syndrome group B (CSB) protein.
Title: Current and emerging roles of Cockayne syndrome group B (CSB) protein.

Submit: New GeneRIF Correction See all GeneRIFs (145)

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
Age-related macular degeneration 5 MedGen: C3151063 OMIM: 613761 GeneReviews: Not available	Compare labs
Cerebrooculofacioskeletal syndrome 1 MedGen: C0220722 OMIM: 214150 GeneReviews: Not available	Compare labs
Cockayne syndrome B MedGen: C0751038 OMIM: 133540 GeneReviews: Cockayne Syndrome	Compare labs
DE SANCTIS-CACCHIONE SYNDROME MedGen: C0265201 OMIM: 278800 GeneReviews: Not available	Compare labs
Lung cancer MedGen: C0242379 OMIM: 211980 GeneReviews: Not available	Compare labs
Premature ovarian failure 11 MedGen: C4310783 OMIM: 616946 GeneReviews: Not available	Compare labs
UV-sensitive syndrome 1 MedGen: C3551173 OMIM: 600630 GeneReviews: Not available	Compare labs

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

RH104261 (e-PCR)
- UniSTS:98586

G60405 (e-PCR)
- UniSTS:137511

D10S1321E (e-PCR)
- UniSTS:151349

RH26695 (e-PCR)
- UniSTS:89910

D10S1553 (e-PCR)
- UniSTS:19011

D10S1378E (e-PCR)
- UniSTS:151374

ERCC6_1944 (e-PCR)
- UniSTS:280657

D10S1766 (e-PCR)
- UniSTS:67929

SHGC-37683 (e-PCR)
- UniSTS:2923

SHGC-67307 (e-PCR)
- UniSTS:89991

RH66662 (e-PCR)
- UniSTS:58254

RH44808 (e-PCR)
- UniSTS:61612

STS-L04791 (e-PCR)
- UniSTS:8116

RH92205 (e-PCR)
- UniSTS:92088

D10S238E (e-PCR)
- UniSTS:147404

SHGC-149029 (e-PCR)
- UniSTS:182235

RH98308 (e-PCR)
- UniSTS:85980

D10S2351 (e-PCR)
- UniSTS:23293

Homology

Homologs of the ERCC6 gene: The ERCC6 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, and zebrafish.
Orthologs from Annotation Pipeline: 407 organisms have orthologs with human gene ERCC6
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on DNA	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables ATP-dependent activity, acting on DNA	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent activity, acting on DNA	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP-dependent chromatin remodeler activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
NOT enables DNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein C-terminus binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein N-terminus binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein tyrosine kinase activator activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA protection	IEA Inferred from Electronic Annotation more info
involved_in JNK cascade	IEA Inferred from Electronic Annotation more info
involved_in base-excision repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair via classical nonhomologous end joining	IDA Inferred from Direct Assay more info	PubMed
involved_in intrinsic apoptotic signaling pathway in response to DNA damage	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of double-strand break repair via nonhomologous end joining	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA repair	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription, elongation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of double-strand break repair via homologous recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein tyrosine kinase activity	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase III	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription initiation from RNA polymerase II promoter	IEA Inferred from Electronic Annotation more info
involved_in pyrimidine dimer repair	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription, elongation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription elongation from RNA polymerase II promoter	IEA Inferred from Electronic Annotation more info
involved_in response to UV	IDA Inferred from Direct Assay more info	PubMed
involved_in response to UV-B	IEA Inferred from Electronic Annotation more info
involved_in response to X-ray	IEA Inferred from Electronic Annotation more info
involved_in response to gamma radiation	IEA Inferred from Electronic Annotation more info
involved_in response to oxidative stress	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to oxidative stress	IGI Inferred from Genetic Interaction more info	PubMed
involved_in response to superoxide	IEA Inferred from Electronic Annotation more info
involved_in response to toxic substance	IEA Inferred from Electronic Annotation more info
involved_in single strand break repair	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in transcription elongation from RNA polymerase I promoter	IEA Inferred from Electronic Annotation more info
involved_in transcription-coupled nucleotide-excision repair	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in transcription-coupled nucleotide-excision repair	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of B-WICH complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in site of DNA damage	IDA Inferred from Direct Assay more info	PubMed
part_of transcription elongation factor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: DNA excision repair protein ERCC-6; ERCC6-PGBD3 fusion protein

Names: ATP-dependent helicase ERCC6; Chimeric CSB-PGBD3 protein; Chimeric ERCC6-PGBD3 protein; Cockayne syndrome group B protein; cockayne syndrome protein CSB; excision repair cross-complementation group 6; excision repair cross-complementing rodent repair deficiency, complementation group 6

NP_000115.1

EC 3.6.4.-

NP_001263987.1

EC 3.6.4.-

NP_001263988.1

EC 3.6.4.-

NP_001333369.1

EC 3.6.4.-

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_009442.1 RefSeqGene

Range

4979..89622

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_465

mRNA and Protein(s)

NM_000124.4 → NP_000115.1 DNA excision repair protein ERCC-6 isoform 2

See identical proteins and their annotated locations for NP_000115.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longer protein (isoform 2).

Source sequence(s)

AB209504, AC073366, AL138760, DA457690, L04791

Consensus CDS

CCDS7229.1

UniProtKB/Swiss-Prot

Q03468

UniProtKB/TrEMBL

Q59FF6

Related

ENSP00000348089.5, ENST00000355832.10

Conserved Domains (3) summary

cd00046
Location:527 → 677

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.

cd00079
Location:830 → 960

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:510 → 812

SNF2_N; SNF2 family N-terminal domain
NM_001277058.2 → NP_001263987.1 ERCC6-PGBD3 fusion protein isoform 1

See identical proteins and their annotated locations for NP_001263987.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) contains an alternate 3' terminal exon, compared to variant 3. It is generated as a result of splicing of ERCC6 exon 5 to the 3' splice site upstream of the PGBD3 ORF that activates the alternative polyadenylation site downstream of the PGBD3 ORF. The resulting protein (isoform 1, ERCC6-PGBD3 fusion protein) is shorter and has a distinct C-terminus, compared to isoform 2.

Source sequence(s)

AC073366, AK291018, AL138760

Consensus CDS

CCDS60529.1

UniProtKB/Swiss-Prot

P0DP91

UniProtKB/TrEMBL

A8K4Q3

Related

ENSP00000387966.2, ENST00000447839.7

Conserved Domains (3) summary

pfam13843
Location:609 → 967

DDE_Tnp_1_7; Transposase IS4

cd21397
Location:83 → 159

cc_ERCC-6_N; coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins

cl00040
Location:1019 → 1055

C1; protein kinase C conserved region 1 (C1 domain) superfamily
NM_001277059.2 → NP_001263988.1 ERCC6-PGBD3 fusion protein isoform 1

See identical proteins and their annotated locations for NP_001263988.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and contains an alternate 3' terminal exon, compared to variant 3. It is generated as a result of splicing of ERCC6 exon 5 to the 3' splice site upstream of the PGBD3 ORF that activates the alternative polyadenylation site downstream of the PGBD3 ORF. The resulting protein (isoform 1, ERCC6-PGBD3 fusion protein) is shorter and has a distinct C-terminus, compared to isoform 2.

Source sequence(s)

AK291018, AL138760, BC034479

Consensus CDS

CCDS60529.1

UniProtKB/Swiss-Prot

P0DP91

UniProtKB/TrEMBL

A8K4Q3

Related

ENSP00000423550.1, ENST00000515869.1

Conserved Domains (3) summary

pfam13843
Location:609 → 967

DDE_Tnp_1_7; Transposase IS4

cd21397
Location:83 → 159

cc_ERCC-6_N; coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins

cl00040
Location:1019 → 1055

C1; protein kinase C conserved region 1 (C1 domain) superfamily
NM_001346440.2 → NP_001333369.1 DNA excision repair protein ERCC-6 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (4 ) uses an alternate splice site in the 5' UTR, compared to variant 3, and encodes isoform 2. Variants 3 and 4 encode the same protein (isoform 2).

Source sequence(s)

AC073366, AL138760, DA457690, L04791

Consensus CDS

CCDS7229.1

UniProtKB/Swiss-Prot

Q03468