ERCC3

protein-coding

ERCC 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

NM_000122.2

Inheritance

AR, AD

ClinVar variants

P:68U:269B:186

Top phenotype

Xeroderma pigmentosum, complementation group B; Trichothiodystrophy 2, photosensitive

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr2:127,257,290-127,294,166

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~36.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

trichothiodystrophySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0018053

Submitter: Orphanet

xeroderma pigmentosum group BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012531

Submitter: G2P

trichothiodystrophy 2, photosensitiveLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014615

Submitter: Labcorp Genetics (formerly Invitae)

xeroderma pigmentosum group BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012531

Submitter: Labcorp Genetics (formerly Invitae)

xeroderma pigmentosum group BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012531

Submitter: Genomics England PanelApp

trichothiodystrophy 1, photosensitiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011125

Submitter: Genomics England PanelApp

xeroderma pigmentosumSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019600

Submitter: Orphanet

hereditary breast carcinomaNO_KNOWN

Inheritance Pattern: AD

Disease ID:MONDO:0016419

Submitter: Ambry Genetics

trichothiodystrophy 2, photosensitiveDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014615

Submitter: G2P

xeroderma pigmentosum-Cockayne syndrome complexSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016354

Submitter: Orphanet

trichothiodystrophy 2, photosensitiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014615

Submitter: PanelApp Australia

xeroderma pigmentosum group BDEFINITIVE

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)

Xeroderma pigmentosum, complementation group B; Trichothiodystrophy 2, photosensitiveAR

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

Refs: 4811796; 6185841; 2189905; 2167179; 8783572; 9012405; 16947863; 20301571Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ERCC3 variants in ClinVar

11 Conditions Cataloged
not providedTotal: 550
Xeroderma pigmentosum group BTotal: 90
Inborn genetic diseasesTotal: 82
Xeroderma pigmentosumTotal: 59
not specifiedTotal: 58
Trichothiodystrophy 2, photosensitiveTotal: 42
ERCC3-related disorderTotal: 25
Ovarian cancerTotal: 7

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
174
clinvar
179
missense
2
clinvar
2
clinvar
257
clinvar
8
clinvar
4
clinvar
273
nonsense
14
clinvar
11
clinvar
1
clinvar
26
start loss
2
clinvar
2
frameshift
17
clinvar
12
clinvar
1
clinvar
30
splice donor/acceptor (+/-2bp)
1
clinvar
7
clinvar
5
clinvar
13
Total34342691824523

Highest pathogenic variant AF is 0.00034331423

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000122.2RefSeqNP_000113.115MANE Select
ENST00000285398.7EnsemblENSP00000285398.215MANE Select
NM_001303416.2RefSeqNP_001290345.114Standard
NM_001303418.2RefSeqNP_001290347.114Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.9323794340.8740.00002585165
Missense (PolyPhen)123162.770.755661937
Synonymous0.3281641690.9680.00001061483
Loss of Function2.682443.00.5590.00000276463

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000740.00074rare
Latino/Admixed American0.000780.00078rare
Ashkenazi Jewish0.00910.0092notable
East Asian0.000430.00044rare
Finnish0.000190.00018rare
European (Non-Finnish)0.00110.0011notable
South Asian0.000520.00052rare
Other0.00150.0015notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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