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NM_004628.5(XPC):c.779+1G>A AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 24, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003558514.2

Allele description [Variation Report for NM_004628.5(XPC):c.779+1G>A]

NM_004628.5(XPC):c.779+1G>A

Gene:
XPC:XPC complex subunit, DNA damage recognition and repair factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.1
Genomic location:
Preferred name:
NM_004628.5(XPC):c.779+1G>A
HGVS:
  • NC_000003.12:g.14165427C>T
  • NG_011763.1:g.18246G>A
  • NM_001354726.2:c.200+1G>A
  • NM_001354727.2:c.779+1G>A
  • NM_001354729.2:c.761+1G>A
  • NM_001354730.2:c.779+1G>A
  • NM_004628.5:c.779+1G>AMANE SELECT
  • LRG_472t1:c.779+1G>A
  • LRG_472:g.18246G>A
  • NC_000003.11:g.14206927C>T
  • NM_004628.4:c.779+1G>A
Links:
dbSNP: rs975121308
NCBI 1000 Genomes Browser:
rs975121308
Molecular consequence:
  • NM_001354726.2:c.200+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354727.2:c.779+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354729.2:c.761+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354730.2:c.779+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004628.5:c.779+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004292211Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Nov 24, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Further evidence of mutational heterogeneity of the XPC gene in Tunisian families: a spectrum of private and ethnic specific mutations.

Ben Rekaya M, Jerbi M, Messaoud O, Ben Brick AS, Zghal M, Mbarek C, Chadli-Debbiche A, Jones M, Mokni M, Boussen H, Boubaker MS, Fazaa B, Yacoub-Youssef H, Abdelhak S.

Biomed Res Int. 2013;2013:316286. doi: 10.1155/2013/316286. Epub 2013 Jul 25.

PubMed [citation]
PMID:
23984341
PMCID:
PMC3741899

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004292211.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Studies have shown that disruption of this splice site results in loss of the splicing donor site and introduces a premature termination codon (PMID: 23984341). The resulting mRNA is expected to undergo nonsense-mediated decay. ClinVar contains an entry for this variant (Variation ID: 555583). Disruption of this splice site has been observed in individual(s) with Xeroderma pigmentosum (PMID: 23984341). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 6 of the XPC gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024