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NM_000124.4(ERCC6):c.1398-2A>G

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 13, 2019
Accession:
VCV000554946.3
Variation ID:
554946
Description:
single nucleotide variant
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NM_000124.4(ERCC6):c.1398-2A>G

Allele ID
545454
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q11.23
Genomic location
10: 49506014 (GRCh38) GRCh38 UCSC
10: 50714060 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_465:g.38088A>G
LRG_465t1:c.1398-2A>G
NC_000010.10:g.50714060T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:49506013:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
Links
dbSNP: rs1317145066
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Nov 9, 2017 RCV000670670.1
Likely pathogenic 1 criteria provided, single submitter Dec 13, 2019 RCV001035343.2
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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
531 825

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Nov 09, 2017)
criteria provided, single submitter
Method: clinical testing
Cockayne syndrome B
Cerebrooculofacioskeletal syndrome 1
DE SANCTIS-CACCHIONE SYNDROME
Allele origin: unknown
Counsyl
Accession: SCV000795554.1
Submitted: (Jul 10, 2018)
Evidence details
Likely pathogenic
(Dec 13, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001198668.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change affects an acceptor splice site in intron 5 of the ERCC6 gene. It is expected to disrupt RNA splicing and likely results … (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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Title Author Journal Year Link
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
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Molecular analysis of mutations in the CSB (ERCC6) gene in patients with Cockayne syndrome. Mallery DL American journal of human genetics 1998 PMID: 9443879

Text-mined citations for rs1317145066...

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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 27, 2021