NM_004628.5(XPC):c.2010T>A (p.Cys670Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 18, 2022
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:: RCV001941958.4

Allele description [Variation Report for NM_004628.5(XPC):c.2010T>A (p.Cys670Ter)]

NM_004628.5(XPC):c.2010T>A (p.Cys670Ter)

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.2010T>A (p.Cys670Ter)

HGVS:

NC_000003.12:g.14156358A>T
NG_011763.1:g.27315T>A
NM_001354726.2:c.1431T>A
NM_001354727.2:c.1872+1653T>A
NM_001354729.2:c.1992T>A
NM_001354730.2:c.1764T>A
NM_004628.5:c.2010T>AMANE SELECT
NP_001341655.1:p.Cys477Ter
NP_001341658.1:p.Cys664Ter
NP_001341659.1:p.Cys588Ter
NP_004619.3:p.Cys670Ter
LRG_472:g.27315T>A
NC_000003.11:g.14197858A>T

Protein change:

C477*

Links:

dbSNP: rs781023624

NCBI 1000 Genomes Browser:

rs781023624

Molecular consequence:

NM_001354727.2:c.1872+1653T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354726.2:c.1431T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354729.2:c.1992T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354730.2:c.1764T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_004628.5:c.2010T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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NADH dehydrogenase subunit 4 (mitochondrion) [Lenzites betulinus]
NADH dehydrogenase subunit 4 (mitochondrion) [Lenzites betulinus]
gi|2743647021|gb|XBS50038.1|

Protein
Macrolepiota subsquarrosa isolate HAI-C-339 18S ribosomal RNA gene, partial sequ...
Macrolepiota subsquarrosa isolate HAI-C-339 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
gi|383465392|gb|JQ683104.1|

Nucleotide
Cymatoderma elegans voucher Yuan 19343 small subunit ribosomal RNA gene, partial...
Cymatoderma elegans voucher Yuan 19343 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|2812704549|gb|PQ415520.1|

Nucleotide
ATP synthase F0 subunit 6 (mitochondrion) [Lenzites betulinus]
ATP synthase F0 subunit 6 (mitochondrion) [Lenzites betulinus]
gi|2743647027|gb|XBS50044.1|

Protein
Cymatoderma dendriticum voucher GXU 12262 internal transcribed spacer 1, partial...
Cymatoderma dendriticum voucher GXU 12262 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|2550991051|gb|OR342204.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002233119	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 18, 2022)	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

SCV002233119

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 18, 2022)

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, SCV002233119.3

#	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.Cys670*) 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 not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with XPC-related conditions. 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

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