ERCC4

protein-coding

ERCC 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]

Previous symbols:
  • XPF

MANE transcript

NM_005236.3

Inheritance

AR

ClinVar variants

P:75U:499B:240

Top phenotype

Fanconi anemia, complementation group Q; Xeroderma pigmentosum, complementation group F

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr16:13,920,138-13,952,348

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~32.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Fanconi anemia complementation group QSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014108

Submitter: G2P

Fanconi anemiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019391

Submitter: Orphanet

xeroderma pigmentosumSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019600

Submitter: Orphanet

xeroderma pigmentosum group FSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010215

Submitter: PanelApp Australia

xeroderma pigmentosum group FDEFINITIVE

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.

XFE progeroid syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012590

Submitter: Ambry Genetics

Fanconi anemia complementation group QMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0014108

Submitter: Ambry Genetics

xeroderma pigmentosum-Cockayne syndrome complexSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016354

Submitter: Orphanet

Fanconi anemia complementation group QSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014108

Submitter: Labcorp Genetics (formerly Invitae)

xeroderma pigmentosum group FSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010215

Submitter: Genomics England PanelApp

xeroderma pigmentosum group FDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010215

Submitter: G2P

Clinical Genomic Database (CGD)

Fanconi anemia, complementation group Q; Xeroderma pigmentosum, complementation group FAR

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

Refs: 3834095; 3372781; 2696553; 8427828; 10447254; 17183314; 20301571; 23623386Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ERCC4 variants in ClinVar

24 Conditions Cataloged
Xeroderma pigmentosum, group FTotal: 742
Fanconi anemia complementation group QTotal: 731
Cockayne syndromeTotal: 692
not providedTotal: 164
Inborn genetic diseasesTotal: 110
XFE progeroid syndromeTotal: 85
not specifiedTotal: 73
Xeroderma pigmentosumTotal: 57

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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
211
clinvar
2
clinvar
221
missense
2
clinvar
11
clinvar
478
clinvar
24
clinvar
3
clinvar
518
nonsense
16
clinvar
8
clinvar
3
clinvar
27
start loss
4
clinvar
4
frameshift
13
clinvar
16
clinvar
4
clinvar
33
splice donor/acceptor (+/-2bp)
1
clinvar
8
clinvar
2
clinvar
11
Total32434992355814

Highest pathogenic variant AF is 0.0006288147

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005236.3RefSeqNP_005227.111MANE Select
ENST00000311895.8EnsemblENSP00000310520.711MANE Select
ENST00000462862.1EnsemblENSP00000461322.12Standard
ENST00000574194.1EnsemblENSP00000461883.12Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.7625575091.100.00002945982
Missense (PolyPhen)172161.711.06361892
Synonymous-1.582151881.150.00001071792
Loss of Function2.072539.00.6420.00000213467

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American0.000260.00026rare
Ashkenazi Jewish0.000300.00030rare
East Asian0.000540.00054rare
Finnish0.000140.00014rare
European (Non-Finnish)0.000360.00036rare
South Asian0.000690.00069rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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