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NM_005236.3(ERCC4):c.2647G>A (p.Glu883Lys)

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Interpretation:
Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Mar 31, 2021)
Last evaluated:
Nov 25, 2020
Accession:
VCV000697490.6
Variation ID:
697490
Description:
single nucleotide variant
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NM_005236.3(ERCC4):c.2647G>A (p.Glu883Lys)

Allele ID
688527
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.12
Genomic location
16: 13948243 (GRCh38) GRCh38 UCSC
16: 14042100 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.13948243G>A
NC_000016.9:g.14042100G>A
NM_005236.3:c.2647G>A MANE Select NP_005227.1:p.Glu883Lys missense
... more HGVS
Protein change
E883K
Other names
-
Canonical SPDI
NC_000016.10:13948242:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00011
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
The Genome Aggregation Database (gnomAD), exomes 0.00054
1000 Genomes Project 0.00060
The Genome Aggregation Database (gnomAD) 0.00013
Exome Aggregation Consortium (ExAC) 0.00059
Links
dbSNP: rs201652412
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts May 28, 2019 RCV000989536.2
Likely benign 1 criteria provided, single submitter Nov 25, 2020 RCV000864380.3
Likely benign 1 no assertion criteria provided - RCV001358163.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ERCC4 - - GRCh38
GRCh37
420 441

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Xeroderma pigmentosum, group F
Allele origin: unknown
Mendelics
Accession: SCV001139956.1
Submitted: (Oct 22, 2019)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Xeroderma pigmentosum, group F
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001275988.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia, complementation group Q
Xeroderma pigmentosum, group F
Cockayne syndrome
Allele origin: germline
Invitae
Accession: SCV001005171.3
Submitted: (Jan 07, 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: SCV001553829.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The ERCC4 p.Glu883Lys variant was not identified in the literature nor was it identified in ClinVar or LOVD 3.0. The variant was identified in dbSNP … (more)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs201652412...

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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 May 16, 2021