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NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 30, 2021
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:
RCV000768209.3

Allele description [Variation Report for NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp)]

NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp)

Gene:
ERCC4:ERCC excision repair 4, endonuclease catalytic subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.12
Genomic location:
Preferred name:
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp)
Other names:
R788W
HGVS:
  • NC_000016.10:g.13947991C>T
  • NG_011442.1:g.32835C>T
  • NM_005236.3:c.2395C>TMANE SELECT
  • NP_005227.1:p.Arg799Trp
  • NP_005227.1:p.Arg799Trp
  • LRG_463t1:c.2395C>T
  • LRG_463:g.32835C>T
  • LRG_463p1:p.Arg799Trp
  • NC_000016.9:g.14041848C>T
  • NM_005236.2:c.2395C>T
  • Q92889:p.Arg799Trp
  • p.R799W
Protein change:
R799W; ARG788TRP
Links:
UniProtKB: Q92889#VAR_005850; OMIM: 133520.0002; OMIM: 133520.0011; dbSNP: rs121913049
NCBI 1000 Genomes Browser:
rs121913049
Molecular consequence:
  • NM_005236.3:c.2395C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Xeroderma pigmentosum, group F (XPF)
Synonyms:
XERODERMA PIGMENTOSUM, COMPLEMENTATION GROUP F; XERODERMA PIGMENTOSUM VI; XP, GROUP F; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010215; MedGen: C0268140; OMIM: 278760
Name:
XFE progeroid syndrome (XFEPS)
Identifiers:
MONDO: MONDO:0012590; MedGen: C1970416; OMIM: 610965
Name:
Fanconi anemia complementation group Q
Identifiers:
MONDO: MONDO:0014108; MedGen: C3808988; Orphanet: 84; OMIM: 615272

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000898673Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 30, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV000898673.2

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

Description

ERCC4 NM_005236 exon 11 p.Arg799Trp (c.2395C>T): This variant has been reported in the literature in at least 5 individuals with features or a diagnosis of Xeroderma Pigmentosum-F as compound heterozygous or homozygous (Sijbers 1996 PMID: 8797827, Sijbers 1998 PMID:9579555, Kashiyama 2013 PMID:23623389, Marelli 2016 PMID:27528516, Carre 2017 PMID:28431612). This variant is present in 103/126562 Caucasian individuals in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs121913049). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population and/or variable expressivity. This variant is present in ClinVar (Variation ID:16580). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In addition, functional studies have shown a deleterious effect of this variant (Sijbers 1998 PMID:9579555, de Laat 1998 PMID:9722633). However, these studies may not accurately represent in vivo biological function. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: May 12, 2024