NM_004628.5(XPC):c.1872+1G>C AND Xeroderma pigmentosum, group C

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: May 6, 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:: RCV000680142.7

Allele description [Variation Report for NM_004628.5(XPC):c.1872+1G>C]

NM_004628.5(XPC):c.1872+1G>C

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.1872+1G>C

HGVS:

NC_000003.12:g.14158010C>G
NG_011763.1:g.25663G>C
NM_001354726.2:c.1293+1G>C
NM_001354727.2:c.1872+1G>C
NM_001354729.2:c.1854+1G>C
NM_001354730.2:c.1626+247G>C
NM_004628.5:c.1872+1G>CMANE SELECT
LRG_472t1:c.1872+1G>C
LRG_472:g.25663G>C
NC_000003.11:g.14199510C>G
NM_004628.4:c.1872+1G>C

Links:

dbSNP: rs1559374923

NCBI 1000 Genomes Browser:

rs1559374923

Molecular consequence:

NM_001354730.2:c.1626+247G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354726.2:c.1293+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354727.2:c.1872+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354729.2:c.1854+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_004628.5:c.1872+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV000807587	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 1, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 25326635
SCV001132881	Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	no assertion criteria provided	Likely pathogenic (Jan 29, 2019)	germline	clinical testing
SCV002017953	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 6, 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

SCV000807587

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 1, 2017)

germline

clinical testing

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

SCV001132881

Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City

no assertion criteria provided

Likely pathogenic
(Jan 29, 2019)

germline

clinical testing

SCV002017953

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 6, 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	yes	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

Molecular findings among patients referred for clinical whole-exome sequencing.

Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MR, et al.

JAMA. 2014 Nov 12;312(18):1870-9. doi: 10.1001/jama.2014.14601.

PubMed [citation]

PMID:: 25326635
PMCID:: PMC4326249

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 Baylor Genetics, SCV000807587.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing (GTR000508680.4)	PubMed (2)

Description

This splice site variant is categorized as deleterious according to ACMG guidelines (PMID:18414213) and was found once in our laboratory homozygous in a 15-year-old female with cafe-au-lait spots, freckling, and photosensitivity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided	(GTR000508680.4)	not provided	not provided	not provided	not provided

From Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City, SCV001132881.1

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

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

From Revvity Omics, Revvity, SCV002017953.3

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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