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NM_004628.5(XPC):c.1780C>T (p.Arg594Cys) AND not provided

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Jan 31, 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:
RCV000861309.9

Allele description [Variation Report for NM_004628.5(XPC):c.1780C>T (p.Arg594Cys)]

NM_004628.5(XPC):c.1780C>T (p.Arg594Cys)

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.1780C>T (p.Arg594Cys)
HGVS:
  • NC_000003.12:g.14158103G>A
  • NG_011763.1:g.25570C>T
  • NM_001354726.2:c.1201C>T
  • NM_001354727.2:c.1780C>T
  • NM_001354729.2:c.1762C>T
  • NM_001354730.2:c.1626+154C>T
  • NM_004628.5:c.1780C>TMANE SELECT
  • NP_001341655.1:p.Arg401Cys
  • NP_001341656.1:p.Arg594Cys
  • NP_001341658.1:p.Arg588Cys
  • NP_004619.3:p.Arg594Cys
  • NP_004619.3:p.Arg594Cys
  • LRG_472t1:c.1780C>T
  • LRG_472:g.25570C>T
  • LRG_472p1:p.Arg594Cys
  • NC_000003.11:g.14199603G>A
  • NM_004628.4:c.1780C>T
  • NR_148950.2:n.1813C>T
  • NR_148951.2:n.1689C>T
Protein change:
R401C
Links:
dbSNP: rs183238369
NCBI 1000 Genomes Browser:
rs183238369
Molecular consequence:
  • NM_001354730.2:c.1626+154C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354726.2:c.1201C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354727.2:c.1780C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354729.2:c.1762C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004628.5:c.1780C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148950.2:n.1813C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148951.2:n.1689C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001001582Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 31, 2024)
germlineclinical testing

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

SCV005264622Breakthrough Genomics, Breakthrough Genomics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benigngermlinenot provided

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

Summary from all submissions

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

Citations

PubMed

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001001582.6

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

From Breakthrough Genomics, Breakthrough Genomics, SCV005264622.1

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

Last Updated: Sep 29, 2024