NM_004628.5(XPC):c.1750_1751del (p.Arg584fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 13, 2024
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:: RCV003669167.2

Allele description [Variation Report for NM_004628.5(XPC):c.1750_1751del (p.Arg584fs)]

NM_004628.5(XPC):c.1750_1751del (p.Arg584fs)

Gene:

XPC:XPC complex subunit, DNA damage recognition and repair factor [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_004628.5(XPC):c.1750_1751del (p.Arg584fs)

HGVS:

NC_000003.12:g.14158132CT[1]
NG_011763.1:g.25538AG[1]
NM_001354726.2:c.1171_1172del
NM_001354727.2:c.1750_1751del
NM_001354729.2:c.1732_1733del
NM_001354730.2:c.1626+124_1626+125del
NM_004628.5:c.1750_1751delMANE SELECT
NP_001341655.1:p.Arg391fs
NP_001341656.1:p.Arg584fs
NP_001341658.1:p.Arg578fs
NP_004619.3:p.Arg584fs
LRG_472:g.25538AG[1]
NC_000003.11:g.14199632CT[1]
NC_000003.11:g.14199632_14199633del
NM_004628.4:c.1750_1751delAG
NR_148950.2:n.1781AG[1]
NR_148951.2:n.1657AG[1]

Protein change:

R391fs

Links:

dbSNP: rs752030576

NCBI 1000 Genomes Browser:

rs752030576

Molecular consequence:

NM_001354726.2:c.1171_1172del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354727.2:c.1750_1751del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354729.2:c.1732_1733del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004628.5:c.1750_1751del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354730.2:c.1626+124_1626+125del - intron variant - [Sequence Ontology: SO:0001627]
NR_148950.2:n.1781AG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148951.2:n.1657AG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus interleukin 25 (Il25), mRNA
Mus musculus interleukin 25 (Il25), mRNA
gi|298676501|ref|NM_080729.3|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004388981	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 13, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23173980, 25256075, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004388981

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 13, 2024)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular genetic analysis of 16 XP-C patients from Germany: environmental factors predominately contribute to phenotype variations.

Schäfer A, Hofmann L, Gratchev A, Laspe P, Schubert S, Schürer A, Ohlenbusch A, Tzvetkov M, Hallermann C, Reichrath J, Schön MP, Emmert S.

Exp Dermatol. 2013 Jan;22(1):24-9. doi: 10.1111/exd.12052. Epub 2012 Nov 22.

PubMed [citation]

PMID:: 23173980

Genotype-phenotype correlation of xeroderma pigmentosum in a Chinese Han population.

Sun Z, Zhang J, Guo Y, Ni C, Liang J, Cheng R, Li M, Yao Z.

Br J Dermatol. 2015 Apr;172(4):1096-102. doi: 10.1111/bjd.13429. Epub 2015 Feb 27.

PubMed [citation]

PMID:: 25256075

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004388981.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Arg584Valfs*15) in the XPC gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in XPC are known to be pathogenic (PMID: 23173980, 25256075). This variant is present in population databases (rs752030576, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with XPC-related conditions. ClinVar contains an entry for this variant (Variation ID: 555204). For these reasons, this variant has been classified as Pathogenic.

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine