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NM_000124.4(ERCC6):c.2599-26A>G AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 11, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001236817.5

Allele description [Variation Report for NM_000124.4(ERCC6):c.2599-26A>G]

NM_000124.4(ERCC6):c.2599-26A>G

Gene:
ERCC6:ERCC excision repair 6, chromatin remodeling factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q11.23
Genomic location:
Preferred name:
NM_000124.4(ERCC6):c.2599-26A>G
HGVS:
  • NC_000010.11:g.49473613T>C
  • NG_009442.1:g.70489A>G
  • NM_000124.4:c.2599-26A>GMANE SELECT
  • NM_001346440.2:c.2599-26A>G
  • LRG_465t1:c.2599-26A>G
  • LRG_465:g.70489A>G
  • NC_000010.10:g.50681659T>C
  • NM_000124.2:c.2599-26A>G
  • NM_000124.3:c.2599-26A>G
Links:
dbSNP: rs4253196
NCBI 1000 Genomes Browser:
rs4253196
Molecular consequence:
  • NM_000124.4:c.2599-26A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001346440.2:c.2599-26A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001409554Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 11, 2024)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Mutation update for the CSB/ERCC6 and CSA/ERCC8 genes involved in Cockayne syndrome.

Laugel V, Dalloz C, Durand M, Sauvanaud F, Kristensen U, Vincent MC, Pasquier L, Odent S, Cormier-Daire V, Gener B, Tobias ES, Tolmie JL, Martin-Coignard D, Drouin-Garraud V, Heron D, Journel H, Raffo E, Vigneron J, Lyonnet S, Murday V, Gubser-Mercati D, Funalot B, et al.

Hum Mutat. 2010 Feb;31(2):113-26. doi: 10.1002/humu.21154.

PubMed [citation]
PMID:
19894250

Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing.

Calmels N, Greff G, Obringer C, Kempf N, Gasnier C, Tarabeux J, Miguet M, Baujat G, Bessis D, Bretones P, Cavau A, Digeon B, Doco-Fenzy M, Doray B, Feillet F, Gardeazabal J, Gener B, Julia S, Llano-Rivas I, Mazur A, Michot C, Renaldo-Robin F, et al.

Orphanet J Rare Dis. 2016 Mar 22;11:26. doi: 10.1186/s13023-016-0408-0.

PubMed [citation]
PMID:
27004399
PMCID:
PMC4804614
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001409554.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change falls in intron 13 of the ERCC6 gene. It does not directly change the encoded amino acid sequence of the ERCC6 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs4253196, gnomAD 0.01%). This variant has been observed in individual(s) with Cockayne syndrome (PMID: 19894250, 27004399, 29572252). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 190162). Studies have shown that this variant results in partial insertion of intron 13 into the mRNA and introduces a premature termination codon (PMID: 9443879, 29572252). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Mar 10, 2024