NM_000124.4(ERCC6):c.1717_1720del (p.Cys573fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 30, 2022
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:: RCV002810738.3

Allele description [Variation Report for NM_000124.4(ERCC6):c.1717_1720del (p.Cys573fs)]

NM_000124.4(ERCC6):c.1717_1720del (p.Cys573fs)

Gene:

ERCC6:ERCC excision repair 6, chromatin remodeling factor [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10q11.23

Genomic location:

Preferred name:

NM_000124.4(ERCC6):c.1717_1720del (p.Cys573fs)

HGVS:

NC_000010.11:g.49493218GACA[1]
NG_009442.1:g.50877TGTC[1]
NM_000124.4:c.1717_1720delMANE SELECT
NM_001346440.2:c.1717_1720del
NP_000115.1:p.Cys573Glnfs
NP_000115.1:p.Cys573fs
NP_001333369.1:p.Cys573fs
LRG_465t1:c.1713_1716TGTC[1]
LRG_465:g.50877TGTC[1]
LRG_465p1:p.Cys573Glnfs
NC_000010.10:g.50701264GACA[1]
NC_000010.10:g.50701264_50701267del
NM_000124.2:c.1713_1716TGTC[1]

Protein change:

C573fs

Molecular consequence:

NM_000124.4:c.1717_1720del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001346440.2:c.1717_1720del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003209592	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 30, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18628313, 29572252, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003209592

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 30, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Cerebro-oculo-facio-skeletal syndrome: three additional cases with CSB mutations, new diagnostic criteria and an approach to investigation.

Laugel V, Dalloz C, Tobias ES, Tolmie JL, Martin-Coignard D, Drouin-Garraud V, Valayannopoulos V, Sarasin A, Dollfus H.

J Med Genet. 2008 Sep;45(9):564-71. doi: 10.1136/jmg.2007.057141. Epub 2008 Jul 15.

PubMed [citation]

PMID:: 18628313

Functional and clinical relevance of novel mutations in a large cohort of patients with Cockayne syndrome.

Calmels N, Botta E, Jia N, Fawcett H, Nardo T, Nakazawa Y, Lanzafame M, Moriwaki S, Sugita K, Kubota M, Obringer C, Spitz MA, Stefanini M, Laugel V, Orioli D, Ogi T, Lehmann AR.

J Med Genet. 2018 May;55(5):329-343. doi: 10.1136/jmedgenet-2017-104877. Epub 2018 Mar 23.

PubMed [citation]

PMID:: 29572252

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003209592.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with ERCC6-related conditions. This variant is present in population databases (rs766629930, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Cys573Glnfs*4) in the ERCC6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ERCC6 are known to be pathogenic (PMID: 18628313, 29572252).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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