ERCC3
protein-codingERCC excision repair 3, TFIIH core complex helicase subunit, the group of Xeroderma pigmentosum complementation groups|DNA helicases|ERCC excision repair associated|General transcription factor IIH complex subunits
Gene summary
This gene encodes an ATP-dependent DNA helicase that functions in nucleotide excision repair. The encoded protein is a subunit of basal transcription factor 2 (TFIIH) and, therefore, also functions in class II transcription. Mutations in this gene are associated with Xeroderma pigmentosum B, Cockayne's syndrome, and trichothiodystrophy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0018053
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012531
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0014615
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0012531
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0012531
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0011125
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0019600
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0016419
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014615
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0016354
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014615
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0012531
Submitter: ClinGen
There is abundant evidence published associating the ERCC3 gene with xeroderma pigmentosum group B since the gene-disease relationship was first proposed by Weeda et al. (1990). Multiple case level studies have been performed with XPB patients that have variants in the ERCC3 gene. Although germline ERCC3 variants are rare, eight known disease-causing mutations from six patients have been reported to date. 8 complementation groups genes (XPA, XPB, XPC, XPD, XPE, XPF, XPG, and XP variant (XPV)) in Nucleotide excision repair (NER) pathway were reported to cause Xeroderma Pigmentosum. Studies of patient-derived cells showed decreased DNA repair rates and decreased levels of XPB protein. An Xpb mouse model for combined xeroderma pigmentosum and cockayne syndrome has been established to show consistent phenotypes with XPB patients by recapitulating the UV sensitivity. All of these types of evidence are consistent with a definitive relationship between the ERCC3 gene and xeroderma pigmentosum group B.
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Dermatologic; Endocrine; Genitourinary; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic
Intervention: Allergy/Immunology/Infectious; Dermatologic; Oncologic
Rationale: In Trichothiodystrophy, individuals may be at high risk for skin cancer, and preventive measures may be beneficial; Frequent infections have been reported, and prophylaxis and early and aggressive treatment of infections may be beneficial; In XP, skin lesions can be treated (and possibly prevented in some cases) with a variety of methods, depending on the specific type of lesion; Sun/UV exposure (and other agents, such as tobacco smoke) should be avoided; Periodic surveillance (primarily related to skin manifestations, as well as other sequelae) can be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ERCC3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000122.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | 174 | 179 | |||
| missense | 2 | 2 | 257 | 8 | 4 | 273 |
| nonsense | 14 | 11 | 1 | 26 | ||
| start loss | 2 | 2 | ||||
| frameshift | 17 | 12 | 1 | 30 | ||
| splice donor/acceptor (+/-2bp) | 1 | 7 | 5 | 13 | ||
| Total | 34 | 34 | 269 | 182 | 4 | 523 |
Highest pathogenic variant AF is 0.00034331423
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000113.1 | 15 | MANE Select | |
| Ensembl | ENSP00000285398.2 | 15 | MANE Select | |
| RefSeq | NP_001290345.1 | 14 | Standard | |
| RefSeq | NP_001290347.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nucleotide excision repair - Homo sapiens (human)
- Basal transcription factors - Homo sapiens (human)
- Eukaryotic Transcription Initiation
- DNA Repair
- Disease
Biological Process
- nucleotide-excision repair, DNA duplex unwinding
- response to hypoxia
- DNA topological change
- DNA repair
- transcription-coupled nucleotide-excision repair
Molecular Function
- DNA binding
- damaged DNA binding
- ATP-dependent DNA helicase activity
- helicase activity
- protein kinase activity
Cellular Component
- nucleotide-excision repair factor 3 complex
- transcription factor TFIIH core complex
- nucleus
- nucleoplasm
- transcription factor TFIID complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000285398
- Coding exons
- 15
- Length
- 36887
- Individuals with no LoFs
- 125454
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 294
- Defined
- 125748
- p
- 0.00117
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.932 | 379 | 434 | 0.874 | 0.0000258 | 5165 |
| Missense (PolyPhen) | 123 | 162.77 | 0.75566 | 1937 | ||
| Synonymous | 0.328 | 164 | 169 | 0.968 | 0.0000106 | 1483 |
| Loss of Function | 2.68 | 24 | 43.0 | 0.559 | 0.00000276 | 463 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00074 | 0.00074 | rare |
| Latino/Admixed American | 0.00078 | 0.00078 | rare |
| Ashkenazi Jewish | 0.0091 | 0.0092 | notable |
| East Asian | 0.00043 | 0.00044 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.0011 | 0.0011 | notable |
| South Asian | 0.00052 | 0.00052 | rare |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: ATP-dependent 3'-5' DNA helicase, component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. The ATPase activity of XPB/ERCC3, but not its helicase activity, is required for DNA opening. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. The ATP- dependent helicase activity of XPB/ERCC3 is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module CAK controls the initiation of transcription. {ECO:0000269|PubMed:10024882, ECO:0000269|PubMed:8157004}.;
- Disease
- DISEASE: Xeroderma pigmentosum complementation group B (XP-B) [MIM:610651]: An autosomal recessive pigmentary skin disorder characterized by solar hypersensitivity of the skin, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities. The skin develops marked freckling and other pigmentation abnormalities. Some XP-B patients present features of Cockayne syndrome, including cachectic dwarfism, pigmentary retinopathy, ataxia, decreased nerve conduction velocities. The phenotype combining xeroderma pigmentosum and Cockayne syndrome traits is referred to as XP-CS complex. {ECO:0000269|PubMed:10447254, ECO:0000269|PubMed:16947863, ECO:0000269|PubMed:8304337}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Trichothiodystrophy 2, photosensitive (TTD2) [MIM:616390]: A form of trichothiodystrophy, an autosomal recessive disease characterized by sulfur-deficient brittle hair and multisystem variable abnormalities. The spectrum of clinical features varies from mild disease with only hair involvement to severe disease with cutaneous, neurologic and profound developmental defects. Ichthyosis, intellectual and developmental disabilities, decreased fertility, abnormal characteristics at birth, ocular abnormalities, short stature, and infections are common manifestations. There are both photosensitive and non- photosensitive forms of the disorder. {ECO:0000269|PubMed:9012405}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.268
Intolerance Scores
- LoFtool
- 0.842
- RVIS EVS
- -1.28
- RVIS percentile EVS
- 5.11
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.927
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |