NM_004628.5(XPC):c.2371_2372del (p.Val791fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 26, 2023
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:: RCV003659629.2

Allele description [Variation Report for NM_004628.5(XPC):c.2371_2372del (p.Val791fs)]

NM_004628.5(XPC):c.2371_2372del (p.Val791fs)

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.2371_2372del (p.Val791fs)

HGVS:

NC_000003.12:g.14148611CA[1]
NG_011763.1:g.35060GT[1]
NG_098743.1:g.159CA[1]
NM_001354726.2:c.1792_1793del
NM_001354727.2:c.2365_2366del
NM_001354729.2:c.2353_2354del
NM_001354730.2:c.2125_2126del
NM_004628.5:c.2371_2372delMANE SELECT
NP_001341655.1:p.Val598fs
NP_001341656.1:p.Val789fs
NP_001341658.1:p.Val785fs
NP_001341659.1:p.Val709fs
NP_004619.3:p.Val791Profs
NP_004619.3:p.Val791fs
LRG_472t1:c.2368_2369TG[1]
LRG_472:g.35060GT[1]
LRG_472p1:p.Val791Profs
NC_000003.11:g.14190110_14190111del
NC_000003.11:g.14190111CA[1]
NM_004628.4:c.2368_2369TG[1]
NR_027299.1:n.2348_2349TG[1]
NR_148950.2:n.2241GT[1]
NR_148951.2:n.2117GT[1]

Protein change:

V598fs

Molecular consequence:

NM_001354726.2:c.1792_1793del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354727.2:c.2365_2366del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354729.2:c.2353_2354del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354730.2:c.2125_2126del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004628.5:c.2371_2372del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_148950.2:n.2241GT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148951.2:n.2117GT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004375047	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 26, 2023)	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

SCV004375047

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 26, 2023)

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, SCV004375047.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with XPC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Val791Profs*7) 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).

#	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

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