Xeroderma Pigmentosum via the XPC Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
7349 XPC 81479 81479,81479 $640 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7349XPC81479 81479 $640 Order Options and Pricing

Pricing Comments

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

A 25% additional charge will be applied to STAT orders. View STAT turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

Turnaround Time

18 days on average

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Xeroderma pigmentosum (XP) results in skin changes (blistering due to sunburn in 60% of cases, persistent erythema, freckling, and hyper/hypopigmentation), early onset skin cancers and internal cancers, ocular problems (e.g. severe keratitis, eyelid atrophy, and conjunctival inflammatory masses), and neurologic abnormalities (microcephaly, diminished/absent deep tendon stretch reflexes, progressive sensorineural hearing loss, and cognitive impairment) (Kraemer et al. 2016. PubMed ID: 20301571). The types of cancers involved are usually non-melanoma skin cancers (basal and squamous cell) and cutaneous melanoma. The incidence of skin cancer is 1,000 times the rate of the general population (Webb et al. 2008. PubMed ID: 18292171). Sun exposure must be limited because skin cancer can appear within the first decade of life due to ultraviolet radiation; removal of early pre-cancerous lesions is beneficial. XP occurs in approximately 1 in 250,000 live births in the United States, 2.3 in 1,000,000 live births in Western Europe (Kleijer et al. 2008. PubMed ID: 18329345), and a higher prevalence of 1 in 22,000 live births in Japan (Hirai et al. 2006. PubMed ID: 16905156). Increased rates are also seen in North Africa, and the Middle East, possibly due to increased consanguinity. XP presents with complete penetrance and shows a wide variety of clinical heterogeneity within and between XP groups. This may be due to length of sunlight exposure, complementation group, nature of mutation and unknown factors (Lehmann et al. 2011. PubMed ID: 22044607).

Genetics

Xeroderma pigmentosum is an autosomal recessive disorder caused by biallelic pathogenic variants in the XPA, ERCC3, XPC, ERCC2, DDB2, ERCC1/ERCC4 and ERCC5 genes, which belong to the XPA, XPB, XPC, XPD, XPE, XPF, and XPG complementation groups respectively (DiGiovanna et al. 2012. PubMed ID: 22217736). The products of these genes are involved in DNA repair, specifically nucleotide excision repair (NER). This mechanism of repair is involved in removing UV-induced dipyrimidine photoproducts and chemical crosslinks. If the damage is left unchecked cells have the potential for cancer development. The XP variant phenotype which is caused by POLH variants leads to affected individuals who have an increased skin cancer incidence and eye abnormalities like most XP patients. Cells with POLH variants do not have dysfunctional nucleotide excision repair. Specific genotype-phenotype correlations exist for the XP forms (Kraemer et al. 2016. PubMed ID: 20301571).

The XPC and DDB2 (XPE) protein products are initially required for initial damage detection. Afterwards, the products XPB and XPD open up DNA around the photoproduct. XPA verifies correct protein assembly and then the XPG and XPF nucleases cleave the DNA on either side of the damage for correct repair via the DNA polymerase η (encoded by POLH) (Naegeli et al. 2011. PubMed ID: 21684221; Kraemer et al. 2016. PubMed ID: 20301571). XPF and ERCC1 form a heterodimeric structure-specific endonuclease which is necessary for 5’ cleavage of UV-damaged DNA at the incision step of NER (Kashiyama et al. 2013. PubMed ID: 23623389). Two types of NER are performed within the cell, namely, global genome repair and transcription coupled repair. The former is involved in global genome maintenance, whereas the latter is involved in repair of DNA from transcriptionally active genes. All aforementioned protein products are involved in transcription-coupled repair and most of these gene products are also involved with global genome repair, with the exception of XPC and XPE.

The XPC gene encodes a protein that is a key component of the XPC complex that plays an essential role in early steps of global genome NER. The XPC protein is important for sensing damage in single-stranded DNA (DiGiovanna et al. 2012. PubMed ID: 22217736). Interestingly, patients with XPC or XPE/ DDB2 pathogenic variants do not have severe sunlight lesions and neurological abnormalities, and this may have to do with their type of NER pathway involvement.

To date, more than 100 pathogenic variants have been reported in XPC, with ~87% being related to XP. Of these, 36% are small deletions, 22% are nonsense, 14% splicing. Other less common pathogenic variants include missense (8%), small insertions/duplications (9%), small indels (2%), gross deletions (6%) and gross duplications (2%). One complex rearrangement (1%) has also been reported (Human Genome Mutation Database).

Clinical Sensitivity - Sequencing with CNV PG-Select

Pathogenic variants in XPC account for 43% of XP cases in the US, 31% in Europe, 3% in Japan (Kraemer et al. 2016. PubMed ID: 20301571).

Testing Strategy

This test provides full coverage of all coding exons of the XPC gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Individuals with a clinical presentation of XP. Earlier diagnosis may improve patient prognosis through regular screening and treatment for early-onset malignancies. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in XPC. This test is specifically designed for heritable germline variants and is not appropriate for the detection of somatic variants in tumor tissue.

Gene

Official Gene Symbol OMIM ID
XPC 613208
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Xeroderma Pigmentosum, Complementation Group C AR 278720

Citations

  • DiGiovanna et al. 2012. PubMed ID: 22217736
  • Hirai et al. 2006. PubMed ID: 16905156
  • Human Genome Mutation Database.
  • Kashiyama et al. 2013. PubMed ID: 23623389
  • Kleijer et al. 2008. PubMed ID: 18329345
  • Kraemer et al. 2016. PubMed ID: 20301571
  • Lehmann et al. 2011. PubMed ID: 22044607
  • Naegeli et al. 2011. PubMed ID: 21684221
  • Webb et al. 2008. PubMed ID: 18292171

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

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