ERCC4
protein-codingERCC excision repair 4, endonuclease catalytic subunit, the group of Xeroderma pigmentosum complementation groups|FA complementation groups|ERCC excision repair associated
Gene summary
The protein encoded by this gene forms a complex with ERCC1 and is involved in the 5' incision made during nucleotide excision repair. This complex is a structure specific DNA repair endonuclease that interacts with EME1. Defects in this gene are a cause of xeroderma pigmentosum complementation group F (XP-F), or xeroderma pigmentosum VI (XP6).[provided by RefSeq, Mar 2009]
- XPF
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~32.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014108
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0019391
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0019600
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0010215
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0010215
Submitter: ClinGen
There is abundant evidence published associating the ERCC4 gene with xeroderma pigmentosum group F since the gene-disease relationship was first proposed by Sijbers et al. (1996). Multiple case level studies have been performed with XPF patients that have variants in the ERCC4 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. Studies of patient-derived cells showed reduced nucleotide excision repair activity in GG-NER and TC-NER pathways. An XPF deficient mouse model has been established to show consistent phenotypes with XPF patients including growth retardation and DNA repair defects. All of these types of evidence are consistent with a definitive relationship between the ERCC4 gene and xeroderma pigmentosum group F.
Inheritance Pattern: AR
Disease ID:MONDO:0012590
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014108
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0016354
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014108
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0010215
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0010215
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dermatologic; Endocrine; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic; Renal
Intervention: Cardiovascular; Dermatologic; Hematologic; Oncologic
Rationale: 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; In Fanconi anemia, specific treatments can help manifestations (eg, oral androgens for blood counts; G-CSF for neutrophil count), and awareness of potential cardiac anomalies may enable early identification and management; HSCT can be curative, but solid tumor risk may remain; Surveillance for complications such as bone marrow failure is recommended
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ERCC4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005236.3. 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 | 8 | 211 | 2 | 221 | ||
| missense | 2 | 11 | 478 | 24 | 3 | 518 |
| nonsense | 16 | 8 | 3 | 27 | ||
| start loss | 4 | 4 | ||||
| frameshift | 13 | 16 | 4 | 33 | ||
| splice donor/acceptor (+/-2bp) | 1 | 8 | 2 | 11 | ||
| Total | 32 | 43 | 499 | 235 | 5 | 814 |
Highest pathogenic variant AF is 0.0006288147
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005227.1 | 11 | MANE Select | |
| Ensembl | ENSP00000310520.7 | 11 | MANE Select | |
| Ensembl | ENSP00000461322.1 | 2 | Standard | |
| Ensembl | ENSP00000461883.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fanconi anemia pathway - Homo sapiens (human)
- Nucleotide excision repair - Homo sapiens (human)
- Cyclophosphamide Pathway, Pharmacodynamics
- Nucleotide Excision Repair
- HDR through Single Strand Annealing (SSA)
Biological Process
- resolution of meiotic recombination intermediates
- telomere maintenance
- double-strand break repair via homologous recombination
- DNA repair
- transcription-coupled nucleotide-excision repair
Molecular Function
- single-stranded DNA endodeoxyribonuclease activity
- TFIID-class transcription factor complex binding
- DNA binding
- damaged DNA binding
- single-stranded DNA binding
Cellular Component
- nucleotide-excision repair complex
- nucleotide-excision repair factor 1 complex
- chromosome, telomeric region
- nuclear chromosome, telomeric region
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000311895
- Coding exons
- 11
- Length
- 32189
- Individuals with no LoFs
- 125654
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 94
- Defined
- 125748
- p
- 0.000374
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.762 | 557 | 509 | 1.10 | 0.0000294 | 5982 |
| Missense (PolyPhen) | 172 | 161.71 | 1.0636 | 1892 | ||
| Synonymous | -1.58 | 215 | 188 | 1.15 | 0.0000107 | 1792 |
| Loss of Function | 2.07 | 25 | 39.0 | 0.642 | 0.00000213 | 467 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00054 | 0.00054 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00036 | 0.00036 | rare |
| South Asian | 0.00069 | 0.00069 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalytic component of a structure-specific DNA repair endonuclease responsible for the 5-prime incision during DNA repair. Involved in homologous recombination that assists in removing interstrand cross-link. {ECO:0000269|PubMed:19596235}.;
- Disease
- DISEASE: Xeroderma pigmentosum complementation group F (XP-F) [MIM:278760]: 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. XP-F patients show a mild phenotype. {ECO:0000269|PubMed:10447254, ECO:0000269|PubMed:8797827, ECO:0000269|PubMed:9579555, ECO:0000269|PubMed:9580660}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: XFE progeroid syndrome (XFEPS) [MIM:610965]: A syndrome characterized by aged bird-like facies, lack of subcutaneous fat, dwarfism, cachexia and microcephaly. Additional features include sun-sensitivity from birth, learning disabilities, hearing loss, and visual impairment. {ECO:0000269|PubMed:17183314}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Xeroderma pigmentosum type F/Cockayne syndrome (XPF/CS) [MIM:278760]: A variant form of Cockayne syndrome, a disorder characterized by growth retardation, microcephaly, impairment of nervous system development, pigmentary retinopathy, peculiar facies, and progeria together with abnormal skin photosensitivity. Cockayne syndrome dermatological features are milder than those in xeroderma pigmentosum and skin cancers are not found in affected individuals. XPF/CS patients, however, present with severe skin phenotypes, including severe photosensitivity, abnormal skin pigmentation, and skin cancer predisposition. {ECO:0000269|PubMed:23623389}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Fanconi anemia complementation group Q (FANCQ) [MIM:615272]: A disorder affecting all bone marrow elements and resulting in anemia, leukopenia and thrombopenia. It is associated with cardiac, renal and limb malformations, dermal pigmentary changes, and a predisposition to the development of malignancies. At the cellular level it is associated with hypersensitivity to DNA-damaging agents, chromosomal instability (increased chromosome breakage) and defective DNA repair. {ECO:0000269|PubMed:23623386, ECO:0000269|PubMed:24027083}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.478
Intolerance Scores
- LoFtool
- 0.878
- RVIS EVS
- -0.37
- RVIS percentile EVS
- 28.29
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.952
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |