ERCC2
protein-codingERCC excision repair 2, TFIIH core complex helicase subunit, the group of ERCC excision repair associated|General transcription factor IIH complex subunits|Xeroderma pigmentosum complementation groups|DNA helicases
Gene summary
The nucleotide excision repair pathway is a mechanism to repair damage to DNA. The protein encoded by this gene is involved in transcription-coupled nucleotide excision repair and is an integral member of the basal transcription factor BTF2/TFIIH complex. The gene product has ATP-dependent DNA helicase activity and belongs to the RAD3/XPD subfamily of helicases. Defects in this gene can result in three different disorders, the cancer-prone syndrome xeroderma pigmentosum complementation group D, trichothiodystrophy, and Cockayne syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
- XPD
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0012553
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0011125
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0010212
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0011125
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0010212
Submitter: Laboratory for Molecular Medicine
This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.
Inheritance Pattern: AR
Disease ID:MONDO:0005089
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0008926
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0019600
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0018053
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0010212
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0011125
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0016354
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0010212
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0011125
Submitter: Illumina
Inheritance Pattern: AR
Disease ID:MONDO:0010212
Submitter: ClinGen
There is abundant evidence published associating the ERCC2 gene with xeroderma pigmentosum group D since the gene-disease relationship was first proposed by Frederick et al. (1994). Multiple case level studies have been performed with XPD patients that have variants in the ERCC2 gene. 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. In cells derived from XPD patients, a reduction of the ligand-dependent transactivation mediated by several nuclear receptors and a deficient global genomic NER were observed as functional alteration in patient cells. Xpd mice exhibit severe photosensitivity, cancer predisposition and segmental progeria which are consistent with patient phenotypes. All of these types of evidence are consistent with a definitive relationship between the ERCC2 gene and xeroderma pigmentosum group D.
Inheritance Pattern: AR
Disease ID:MONDO:0010212
Submitter: Genomics England PanelApp
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Craniofacial; 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 can be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ERCC2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000400.4. 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 | 1 | 10 | 628 | 2 | 641 | |
| missense | 6 | 30 | 894 | 20 | 950 | |
| nonsense | 34 | 27 | 2 | 63 | ||
| start loss | 3 | 3 | ||||
| frameshift | 64 | 47 | 7 | 118 | ||
| splice donor/acceptor (+/-2bp) | 6 | 67 | 1 | 74 | ||
| Total | 110 | 172 | 917 | 648 | 2 | 1849 |
Highest pathogenic variant AF is 0.0004461138
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000391.1 | 23 | MANE Select | |
| Ensembl | ENSP00000375809.4 | 23 | MANE Select | |
| RefSeq | NP_001124339.1 | 12 | Standard | |
| RefSeq | NP_001427284.1 | 22 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fluoropyrimidine Pathway, Pharmacodynamics
- Nucleotide excision repair - Homo sapiens (human)
- Doxorubicin Pathway (Cancer Cell), Pharmacodynamics
- Basal transcription factors - Homo sapiens (human)
- Nucleotide Excision Repair
Biological Process
- regulation of mitotic recombination
- nucleotide-excision repair, DNA duplex unwinding
- response to hypoxia
- in utero embryonic development
- transcription-coupled nucleotide-excision repair
Molecular Function
- damaged DNA binding
- ATP-dependent DNA helicase activity
- protein kinase activity
- protein binding
- ATP binding
Cellular Component
- transcription factor TFIIH core complex
- nucleus
- nucleoplasm
- transcription factor TFIID complex
- transcription factor TFIIH holo complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000391945
- Coding exons
- 23
- Length
- 21082
- Individuals with no LoFs
- 125582
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 166
- Defined
- 125748
- p
- 0.000660
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.380 | 454 | 477 | 0.951 | 0.0000341 | 4890 |
| Missense (PolyPhen) | 155 | 176.32 | 0.87909 | 1751 | ||
| Synonymous | -2.31 | 247 | 205 | 1.21 | 0.0000148 | 1531 |
| Loss of Function | 1.10 | 34 | 41.7 | 0.816 | 0.00000206 | 477 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00045 | 0.00043 | rare |
| Latino/Admixed American | 0.00044 | 0.00043 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.00037 | 0.00037 | rare |
| European (Non-Finnish) | 0.0010 | 0.0010 | notable |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: ATP-dependent 5'-3' 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 ATP-dependent helicase activity of XPD/ERCC2 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. 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. XPD/ERCC2 acts by forming a bridge between CAK and the core-TFIIH complex. Involved in the regulation of vitamin-D receptor activity. As part of the mitotic spindle-associated MMXD complex it plays a role in chromosome segregation. Might have a role in aging process and could play a causative role in the generation of skin cancers. {ECO:0000269|PubMed:10024882, ECO:0000269|PubMed:15494306, ECO:0000269|PubMed:20797633, ECO:0000269|PubMed:8413672}.;
- Disease
- DISEASE: Xeroderma pigmentosum complementation group D (XP-D) [MIM:278730]: 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-D 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:11709541, ECO:0000269|PubMed:15494306, ECO:0000269|PubMed:7585650, ECO:0000269|PubMed:7825573, ECO:0000269|PubMed:7849702, ECO:0000269|PubMed:9101292}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Trichothiodystrophy 1, photosensitive (TTD1) [MIM:601675]: 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. TTD1 patients manifest cutaneous photosensitivity. {ECO:0000269|PubMed:11242112, ECO:0000269|PubMed:7920640, ECO:0000269|PubMed:8571952, ECO:0000269|PubMed:9195225, ECO:0000269|PubMed:9238033, ECO:0000269|PubMed:9758621}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cerebro-oculo-facio-skeletal syndrome 2 (COFS2) [MIM:610756]: A disorder of prenatal onset characterized by microcephaly, congenital cataracts, facial dysmorphism, neurogenic arthrogryposis, growth failure and severe psychomotor retardation. COFS is considered to be part of the nucleotide-excision repair disorders spectrum that include also xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome. {ECO:0000269|PubMed:11443545}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.771
Intolerance Scores
- LoFtool
- 0.408
- RVIS EVS
- -1.95
- RVIS percentile EVS
- 1.89
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.918
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |