ERCC2

protein-coding

ERCC 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]

Previous symbols:
  • XPD

MANE transcript

NM_000400.4

Inheritance

AR

ClinVar variants

P:282U:917B:650

Top phenotype

Trichothiodystrophy 1, photosensitive; Xeroderma pigmentosum, group D

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr19:45,349,837-45,370,918

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~21.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cerebrooculofacioskeletal syndrome 2DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012553

Submitter: G2P

trichothiodystrophy 1, photosensitiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011125

Submitter: Labcorp Genetics (formerly Invitae)

xeroderma pigmentosum group DDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010212

Submitter: G2P

trichothiodystrophy 1, photosensitiveDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011125

Submitter: G2P

xeroderma pigmentosum group DDEFINITIVE

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.

sarcomaMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0005089

Submitter: Genomics England PanelApp

COFS syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008926

Submitter: Orphanet

xeroderma pigmentosumSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019600

Submitter: Orphanet

trichothiodystrophySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0018053

Submitter: Orphanet

xeroderma pigmentosum group DSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010212

Submitter: PanelApp Australia

trichothiodystrophy 1, photosensitiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011125

Submitter: Genomics England PanelApp

xeroderma pigmentosum-Cockayne syndrome complexSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016354

Submitter: Orphanet

xeroderma pigmentosum group DSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010212

Submitter: Labcorp Genetics (formerly Invitae)

trichothiodystrophy 1, photosensitiveDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011125

Submitter: Illumina

xeroderma pigmentosum group DDEFINITIVE

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.

xeroderma pigmentosum group DSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010212

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Trichothiodystrophy 1, photosensitive; Xeroderma pigmentosum, group DAR

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

Refs: 2189905; 1372108; 7802014; 8783572; 11709541; 11443545; 21959366; 20301571Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ERCC2 variants in ClinVar

24 Conditions Cataloged
not providedTotal: 1299
Inborn genetic diseasesTotal: 1284
Xeroderma pigmentosum, group DTotal: 187
ERCC2-related disorderTotal: 187
Cerebrooculofacioskeletal syndrome 2Total: 185
not specifiedTotal: 162
Trichothiodystrophy 1, photosensitiveTotal: 126
Xeroderma pigmentosumTotal: 87

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
10
clinvar
628
clinvar
2
clinvar
641
missense
6
clinvar
30
clinvar
894
clinvar
20
clinvar
950
nonsense
34
clinvar
27
clinvar
2
clinvar
63
start loss
3
clinvar
3
frameshift
64
clinvar
47
clinvar
7
clinvar
118
splice donor/acceptor (+/-2bp)
6
clinvar
67
clinvar
1
clinvar
74
Total11017291764821849

Highest pathogenic variant AF is 0.0004461138

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000400.4RefSeqNP_000391.123MANE Select
ENST00000391945.10EnsemblENSP00000375809.423MANE Select
NM_001130867.2RefSeqNP_001124339.112Standard
NM_001440355.1RefSeqNP_001427284.122Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3804544770.9510.00003414890
Missense (PolyPhen)155176.320.879091751
Synonymous-2.312472051.210.00001481531
Loss of Function1.103441.70.8160.00000206477

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000450.00043rare
Latino/Admixed American0.000440.00043rare
Ashkenazi Jewish0.000600.00060rare
East Asian0.000330.00033rare
Finnish0.000370.00037rare
European (Non-Finnish)0.00100.0010notable
South Asian0.000200.00020rare
Other0.000650.00065rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerHighMediumHigh
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