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; AllianceGenome:HGNC:3438
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
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (49434881..49539538, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (50283667..50388257, complement)
RS_2024_09	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 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?

Transcription-coupled DNA-protein crosslink repair by CSB and CRL4[CSA]-mediated degradation.
Title: Transcription-coupled DNA-protein crosslink repair by CSB and CRL4(CSA)-mediated degradation.
CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells.
Title: CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells.
CircMAP3K4 Suppresses H2O2-Induced Human Lens Epithelial Cell Injury by miR-630/ERCC6 Axis in Age-Related Cataract.
Title: CircMAP3K4 Suppresses H2O2-Induced Human Lens Epithelial Cell Injury by miR-630/ERCC6 Axis in Age-Related Cataract.
The CSB chromatin remodeler regulates PARP1- and PARP2-mediated single-strand break repair at actively transcribed DNA regions.
Title: The CSB chromatin remodeler regulates PARP1- and PARP2-mediated single-strand break repair at actively transcribed DNA regions.
ERCC6 plays a promoting role in the progression of non-small cell lung cancer.
Title: ERCC6 plays a promoting role in the progression of non-small cell lung cancer.
A novel heterozygous ERCC6 variant identified in a Chinese family with non-syndromic primary ovarian insufficiency.
Title: A novel heterozygous ERCC6 variant identified in a Chinese family with non-syndromic primary ovarian insufficiency.
Genetic pleiotropy of ERCC6 loss-of-function and deleterious missense variants links retinal dystrophy, arrhythmia, and immunodeficiency in diverse ancestries.
Title: Genetic pleiotropy of ERCC6 loss-of-function and deleterious missense variants links retinal dystrophy, arrhythmia, and immunodeficiency in diverse ancestries.
Genetic Association of ERCC6 rs2228526 Polymorphism with the Risk of Cancer: Evidence from a Meta-Analysis.
Title: Genetic Association of ERCC6 rs2228526 Polymorphism with the Risk of Cancer: Evidence from a Meta-Analysis.
MicroRNA Let-7c-5p-Mediated Regulation of ERCC6 Disrupts Autophagic Flux in Age-Related Cataract via the Binding to VCP.
Title: MicroRNA Let-7c-5p-Mediated Regulation of ERCC6 Disrupts Autophagic Flux in Age-Related Cataract via the Binding to VCP.
Profiling and Integrated Analysis of the ERCC6-regulated circRNA-miRNA-mRNA Network in Lens Epithelial Cells.
Title: Profiling and Integrated Analysis of the ERCC6-regulated circRNA-miRNA-mRNA Network in Lens Epithelial Cells.

Submit: New GeneRIF Correction See all GeneRIFs (158)

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	not available
Cerebrooculofacioskeletal syndrome 1 MedGen: C0220722 OMIM: 214150 GeneReviews: Not available	not available
Cockayne syndrome type 2 MedGen: C0751038 OMIM: 133540 GeneReviews: Cockayne Syndrome	not available
DE SANCTIS-CACCHIONE SYNDROME MedGen: C0265201 OMIM: 278800 GeneReviews: Not available	not available
Lung cancer MedGen: C0242379 OMIM: 211980 GeneReviews: Not available	not available
Premature ovarian failure 11 MedGen: C4310783 OMIM: 616946 GeneReviews: Not available	not available
UV-sensitive syndrome 1 MedGen: C3551173 OMIM: 600630 GeneReviews: Not available	not available

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

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 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 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	IBA Inferred from Biological aspect of Ancestor more info
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
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
NOT enables DNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase binding	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 chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
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 sequence-specific DNA binding	IDA Inferred from Direct Assay 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 DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
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 chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	NAS Non-traceable Author Statement 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 defense response to virus by host	IMP Inferred from Mutant Phenotype 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 gene expression	HMP more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of peptidyl-serine phosphorylation of STAT protein	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase I	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
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 by RNA polymerase II	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 by RNA polymerase II	IEA Inferred from Electronic Annotation more info
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 by RNA polymerase I	IEA Inferred from Electronic Annotation more info
involved_in transcription-coupled nucleotide-excision repair	IBA Inferred from Biological aspect of Ancestor more info
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 nuclear body	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	NAS Non-traceable Author Statement 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
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

D3DX94, E7EV46, Q03468, Q5W0L9

UniProtKB/TrEMBL

A0JP10

Related

ENSP00000348089.5, ENST00000355832.10

Conserved Domains (3) summary

COG0553
Location:459 → 1007

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd18000
Location:507 → 694

DEXHc_ERCC6; DEXH-box helicase domain of ERCC6

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
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

D3DX94, E7EV46, Q03468, Q5W0L9

UniProtKB/TrEMBL

A0JP10

Conserved Domains (3) summary

COG0553
Location:459 → 1007

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd18000
Location:507 → 694

DEXHc_ERCC6; DEXH-box helicase domain of ERCC6

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