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NM_000124.4(ERCC6):c.3862C>T (p.Arg1288Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Feb 21, 2021)
Last evaluated:
Oct 13, 2020
Accession:
VCV000031578.8
Variation ID:
31578
Description:
single nucleotide variant
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NM_000124.4(ERCC6):c.3862C>T (p.Arg1288Ter)

Allele ID
40257
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q11.23
Genomic location
10: 49461473 (GRCh38) GRCh38 UCSC
10: 50669519 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.11:g.49461473G>A
NG_009442.1:g.82629C>T
NM_000124.4:c.3862C>T MANE Select NP_000115.1:p.Arg1288Ter nonsense
... more HGVS
Protein change
R1288*
Other names
-
Canonical SPDI
NC_000010.11:49461472:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00014
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD) 0.00025
Exome Aggregation Consortium (ExAC) 0.00006
Links
ClinGen: CA129817
OMIM: 609413.0015
dbSNP: rs185142838
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Oct 13, 2020 RCV000733375.3
Pathogenic 2 criteria provided, single submitter Jun 9, 2020 RCV000024284.6
Pathogenic 1 criteria provided, single submitter Jul 3, 2017 RCV000622864.1
Pathogenic 1 criteria provided, single submitter Nov 30, 2017 RCV000671085.1
Pathogenic 2 criteria provided, single submitter Jan 1, 2019 RCV000784896.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ERCC6 - - GRCh38
GRCh37
529 823

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Nov 30, 2017)
criteria provided, single submitter
Method: clinical testing
Cockayne syndrome B
Cerebrooculofacioskeletal syndrome 1
DE SANCTIS-CACCHIONE SYNDROME
Allele origin: unknown
Counsyl
Accession: SCV000796027.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Pathogenic
(Jun 09, 2020)
criteria provided, single submitter
Method: clinical testing
Cerebrooculofacioskeletal syndrome 1
Allele origin: unknown
Baylor Genetics
Accession: SCV001522601.1
Submitted: (Feb 21, 2021)
Evidence details
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Pathogenic
(Jan 01, 2019)
criteria provided, single submitter
Method: clinical testing
Cockayne syndrome B
Allele origin: inherited
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV000923433.1
Submitted: (Apr 08, 2019)
Evidence details
Pathogenic
(Jul 03, 2017)
criteria provided, single submitter
Method: clinical testing
Inborn genetic diseases
Allele origin: germline
Ambry Genetics
Accession: SCV000742719.2
Submitted: (Oct 09, 2020)
Evidence details
Publications
PubMed (4)
Pathogenic
(May 23, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000861440.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Oct 13, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001219828.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change creates a premature translational stop signal (p.Arg1288*) in the ERCC6 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Dec 01, 2010)
no assertion criteria provided
Method: literature only
CEREBROOCULOFACIOSKELETAL SYNDROME 1
Allele origin: germline
OMIM
Accession: SCV000045575.4
Submitted: (May 17, 2012)
Evidence details
Publications
PubMed (2)
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
Cockayne syndrome B
Allele origin: unknown
Service de Génétique Moléculaire,Hôpital Robert Debré
Accession: SCV001432393.1
Submitted: (Apr 26, 2020)
Evidence details

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
Functional and clinical relevance of novel mutations in a large cohort of patients with Cockayne syndrome. Calmels N Journal of medical genetics 2018 PMID: 29572252
Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing. Calmels N Orphanet journal of rare diseases 2016 PMID: 27004399
Cockayne syndrome: the expanding clinical and mutational spectrum. Laugel V Mechanisms of ageing and development 2013 PMID: 23428416
A possible cranio-oro-facial phenotype in Cockayne syndrome. Bloch-Zupan A Orphanet journal of rare diseases 2013 PMID: 23311583
ERCC6 founder mutation identified in Finnish patients with COFS syndrome. Jaakkola E Clinical genetics 2010 PMID: 20456449
Mutation update for the CSB/ERCC6 and CSA/ERCC8 genes involved in Cockayne syndrome. Laugel V Human mutation 2010 PMID: 19894250
Cerebro-oculo-facio-skeletal syndrome: three additional cases with CSB mutations, new diagnostic criteria and an approach to investigation. Laugel V Journal of medical genetics 2008 PMID: 18628313
Molecular analysis of mutations in the CSB (ERCC6) gene in patients with Cockayne syndrome. Mallery DL American journal of human genetics 1998 PMID: 9443879
Intracranial calcifications in cerebro-oculo-facio-skeletal (COFS) syndrome. Linna SL Pediatric radiology 1982 PMID: 7063265
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ERCC6 - - - -

Text-mined citations for rs185142838...

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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 Oct 30, 2021