NM_000123.4(ERCC5):c.1789G>C (p.Val597Leu) AND Xeroderma pigmentosum, group G

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(2);Uncertain significance(2) (Last evaluated: Nov 3, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000625478.4

Allele description [Variation Report for NM_000123.4(ERCC5):c.1789G>C (p.Val597Leu)]

NM_000123.4(ERCC5):c.1789G>C (p.Val597Leu)

Genes:
BIVM-ERCC5:BIVM-ERCC5 readthrough [Gene - HGNC]
ERCC5:ERCC excision repair 5, endonuclease [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q33.1
Genomic location:
Preferred name:
NM_000123.4(ERCC5):c.1789G>C (p.Val597Leu)
HGVS:
  • NC_000013.11:g.102862938G>C
  • NG_007146.1:g.22115G>C
  • NM_000123.4:c.1789G>CMANE SELECT
  • NM_001204425.2:c.3151G>C
  • NP_000114.2:p.Val597Leu
  • NP_000114.3:p.Val597Leu
  • NP_001191354.2:p.Val1051Leu
  • LRG_464t1:c.1789G>C
  • LRG_464:g.22115G>C
  • LRG_464p1:p.Val597Leu
  • NC_000013.10:g.103515288G>C
  • NM_000123.3:c.1789G>C
  • P28715:p.Val597Leu
Protein change:
V1051L
Links:
UniProtKB: P28715#VAR_023123; dbSNP: rs4150319
NCBI 1000 Genomes Browser:
rs4150319
Molecular consequence:
  • NM_000123.4:c.1789G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001204425.2:c.3151G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Xeroderma pigmentosum, group G (XPG)
Synonyms:
XP, GROUP G; Xeroderma pigmentosum VII; Xeroderma pigmentosum complementation group G; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010216; MedGen: C0268141; OMIM: 278780

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000745529Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensuscriteria provided, single submitter
Likely benign
(Sep 21, 2015)
germlineclinical testing

Citation Link,

SCV000745991Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensuscriteria provided, single submitter
Likely benign
(Apr 29, 2016)
germlineclinical testing

Citation Link,

SCV001268024Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Apr 27, 2017)
germlineclinical testing

Citation Link,

SCV002010215Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresdencriteria provided, single submitter
Uncertain significance
(Nov 3, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745529.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV000745991.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001268024.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002010215.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 4, 2021

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