NM_004628.5(XPC):c.1780C>T (p.Arg594Cys) AND Xeroderma pigmentosum, group C

Germline classification:: Benign (2 submissions)
Last evaluated:: Dec 5, 2021
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:: RCV001150642.5

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)

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001311730	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Nov 14, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002514006	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Dec 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001311730

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Nov 14, 2017)

germline

clinical testing

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

Citation Link,

SCV002514006

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Dec 5, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]

PMID:: 24728327
PMCID:: PMC3984285

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 Illumina Laboratory Services, Illumina, SCV001311730.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002514006.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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