NM_000124.4(ERCC6):c.3650T>G (p.Phe1217Cys) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(3) (Last evaluated: May 24, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000513602.9

Allele description [Variation Report for NM_000124.4(ERCC6):c.3650T>G (p.Phe1217Cys)]

NM_000124.4(ERCC6):c.3650T>G (p.Phe1217Cys)

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.3650T>G (p.Phe1217Cys)
HGVS:
  • NC_000010.11:g.49470310A>C
  • NG_009442.1:g.73792T>G
  • NM_000124.4:c.3650T>GMANE SELECT
  • NM_001346440.2:c.3650T>G
  • NP_000115.1:p.Phe1217Cys
  • NP_001333369.1:p.Phe1217Cys
  • LRG_465t1:c.3650T>G
  • LRG_465:g.73792T>G
  • NC_000010.10:g.50678356A>C
  • NM_000124.2:c.3650T>G
  • NM_000124.3:c.3650T>G
Protein change:
F1217C
Links:
dbSNP: rs61760166
NCBI 1000 Genomes Browser:
rs61760166
Molecular consequence:
  • NM_000124.4:c.3650T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346440.2:c.3650T>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
3

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000343228EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Apr 11, 2017)
germlineclinical testing

Citation Link,

SCV000572273GeneDxcriteria provided, single submitter
Uncertain significance
(May 24, 2021)
germlineclinical testing

Citation Link,

SCV000608537CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(May 1, 2017)
germlineclinical testing

Citation Link,

SCV001015069Invitaecriteria provided, single submitter
Likely benign
(Dec 8, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknown2not providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000343228.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV000572273.4

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

Description

Has been reported in one patient with peripheral neuropathy associated with oxaliplatin (PNAO); this patient harbored a second missense variant in ERCC6 but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (West et al., 2018); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function

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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV000608537.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV001015069.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 30, 2021

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