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NM_004628.5(XPC):c.2331dup (p.Asn778fs) AND Xeroderma pigmentosum, group C

Germline classification:
Likely pathogenic (4 submissions)
Last evaluated:
Jan 5, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000671731.5

Allele description [Variation Report for NM_004628.5(XPC):c.2331dup (p.Asn778fs)]

NM_004628.5(XPC):c.2331dup (p.Asn778fs)

Gene:
XPC:XPC complex subunit, DNA damage recognition and repair factor [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
3p25.1
Genomic location:
Preferred name:
NM_004628.5(XPC):c.2331dup (p.Asn778fs)
HGVS:
  • NC_000003.12:g.14148653dup
  • NG_011763.1:g.35022dup
  • NM_001354726.2:c.1752dup
  • NM_001354727.2:c.2325dup
  • NM_001354729.2:c.2313dup
  • NM_001354730.2:c.2085dup
  • NM_004628.5:c.2331dupMANE SELECT
  • NP_001341655.1:p.Asn585fs
  • NP_001341656.1:p.Asn776fs
  • NP_001341658.1:p.Asn772fs
  • NP_001341659.1:p.Asn696fs
  • NP_004619.3:p.Asn778fs
  • LRG_472:g.35022dup
  • NC_000003.11:g.14190150_14190151insG
  • NC_000003.11:g.14190153dup
  • NM_004628.4:c.2331dupC
  • NR_148950.2:n.2203dup
  • NR_148951.2:n.2079dup
Protein change:
N585fs
Links:
dbSNP: rs1553604552
NCBI 1000 Genomes Browser:
rs1553604552
Molecular consequence:
  • NM_001354726.2:c.1752dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354727.2:c.2325dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354729.2:c.2313dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354730.2:c.2085dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004628.5:c.2331dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_148950.2:n.2203dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148951.2:n.2079dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Xeroderma pigmentosum, group C (XPC)
Synonyms:
XERODERMA PIGMENTOSUM III; XP, GROUP C; Xeroderma pigmentosum, complementation group C
Identifiers:
MONDO: MONDO:0010211; MedGen: C2752147; Orphanet: 910; OMIM: 278720

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000796741Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Likely pathogenic
(Dec 22, 2017)
unknownclinical testing

Citation Link,

SCV004047751Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004207008Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 11, 2023)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005656570Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 5, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Counsyl, SCV000796741.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047751.1

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

Description

The frameshift variant c.2331dup (p.Asn778GlnfsTer21) in XPC gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant has been reported to the ClinVar database as Likely Pathogenic. The p.Asn778GlnfsTer21 variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant causes a frameshift starting with codon Asparagine 778, changes this amino acid to Glutamine residue, and creates a premature Stop codon at position 21 of the new reading frame, denoted p.Asn778GlnfsTer21. This variant is predicted to cause loss of normal protein function. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

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

From Baylor Genetics, SCV004207008.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV005656570.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 1, 2025