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

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Nov 4, 2021)
Last evaluated:
Nov 3, 2021
Accession:
VCV000134195.14
Variation ID:
134195
Description:
single nucleotide variant
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NM_000123.4(ERCC5):c.1789G>C (p.Val597Leu)

Allele ID
137934
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q33.1
Genomic location
13: 102862938 (GRCh38) GRCh38 UCSC
13: 103515288 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P28715:p.Val597Leu
NC_000013.10:g.103515288G>C
NC_000013.11:g.102862938G>C
... more HGVS
Protein change
V597L, V1051L
Other names
-
Canonical SPDI
NC_000013.11:102862937:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00134
1000 Genomes Project 0.00060
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00246
Exome Aggregation Consortium (ExAC) 0.00141
The Genome Aggregation Database (gnomAD) 0.00166
Trans-Omics for Precision Medicine (TOPMed) 0.00178
Links
ClinGen: CA159081
UniProtKB: P28715#VAR_023123
dbSNP: rs4150319
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Sep 25, 2019 RCV001292856.1
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Nov 3, 2021 RCV000625478.4
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Feb 26, 2019 RCV000995081.4
not provided 1 no assertion provided Sep 19, 2013 RCV000120868.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BIVM-ERCC5 - - - GRCh38
GRCh37
- 356
ERCC5 - - GRCh38
GRCh37
3 356

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Xeroderma pigmentosum, group G
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001268024.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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, … (more)
Uncertain significance
(Nov 03, 2021)
criteria provided, single submitter
Method: clinical testing
Xeroderma pigmentosum, group G
Allele origin: germline
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002010215.1
Submitted: (Nov 04, 2021)
Evidence details
Likely benign
(Sep 21, 2015)
criteria provided, single submitter
Method: clinical testing
Xeroderma pigmentosum, group G
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000745529.1
Submitted: (Apr 09, 2018)
Evidence details
Likely benign
(Apr 29, 2016)
criteria provided, single submitter
Method: clinical testing
Xeroderma pigmentosum, group G
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000745991.1
Submitted: (Apr 09, 2018)
Evidence details
Uncertain significance
(Feb 26, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001416378.1
Submitted: (Feb 06, 2020)
Evidence details
Comment:
This sequence change replaces valine with leucine at codon 597 of the ERCC5 protein (p.Val597Leu). The valine residue is weakly conserved and there is a … (more)
Uncertain significance
(Sep 25, 2019)
criteria provided, single submitter
Method: clinical testing
Cerebrooculofacioskeletal syndrome 3
Allele origin: unknown
Baylor Genetics
Study: CSER-TexasKidsCanSeq
Accession: SCV001481536.2
Submitted: (Feb 10, 2021)
Evidence details
Comment:
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Likely benign
(Aug 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001149076.7
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001550118.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The ERCC5 p.Val597Leu variant was not identified in the literature nor was it identified in Cosmic. The variant was identified in dbSNP (ID: rs4150319), ClinVar … (more)
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000085036.1
Submitted: (May 29, 2014)
Comment:
Please see associated publication for description of ethnicities
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327

Text-mined citations for rs4150319...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 06, 2021