NM_000124.4(ERCC6):c.466C>T (p.Gln156Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Jul 2, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000224212.7

Allele description [Variation Report for NM_000124.4(ERCC6):c.466C>T (p.Gln156Ter)]

NM_000124.4(ERCC6):c.466C>T (p.Gln156Ter)

Genes:
ERCC6:ERCC excision repair 6, chromatin remodeling factor [Gene - OMIM - HGNC]
ERCC6-PGBD3:ERCC6-PGBD3 readthrough [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q11.23
Genomic location:
Preferred name:
NM_000124.4(ERCC6):c.466C>T (p.Gln156Ter)
HGVS:
  • NC_000010.11:g.49530797G>A
  • NG_009442.1:g.13305C>T
  • NM_000124.4:c.466C>TMANE SELECT
  • NM_001277058.2:c.466C>T
  • NM_001277059.2:c.466C>T
  • NM_001346440.2:c.466C>T
  • NP_000115.1:p.Gln156Ter
  • NP_001263987.1:p.Gln156Ter
  • NP_001263988.1:p.Gln156Ter
  • NP_001333369.1:p.Gln156Ter
  • LRG_465t1:c.466C>T
  • LRG_465:g.13305C>T
  • NC_000010.10:g.50738843G>A
  • NM_000124.2:c.466C>T
  • NM_000124.3:c.466C>T
  • p.Gln156*
Protein change:
Q156*
Links:
dbSNP: rs751838040
NCBI 1000 Genomes Browser:
rs751838040
Molecular consequence:
  • NM_000124.4:c.466C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001277058.2:c.466C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001277059.2:c.466C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001346440.2:c.466C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000280636Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicscriteria provided, single submitter
Pathogenic
(May 14, 2015)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000329858GeneDxcriteria provided, single submitter
Pathogenic
(May 19, 2020)
germlineclinical testing

Citation Link,

SCV001387855Invitaecriteria provided, single submitter
Pathogenic
(Jul 2, 2020)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

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
See all PubMed Citations (6)

Details of each submission

From Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics, SCV000280636.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.000112not providednot provided

From GeneDx, SCV000329858.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 19894250)

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

From Invitae, SCV001387855.2

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

Description

This sequence change creates a premature translational stop signal (p.Gln156*) in the ERCC6 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs751838040, ExAC 0.001%). This variant has been observed in individuals affected with Cockayne syndrome (PMID: 19894250, 29572252). ClinVar contains an entry for this variant (Variation ID: 212733). Loss-of-function variants in ERCC6 are known to be pathogenic (PMID: 9443879, 18628313). 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: Nov 27, 2021

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