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NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND Xeroderma pigmentosum, group F

Germline classification:
Pathogenic/Likely pathogenic (8 submissions)
Last evaluated:
Feb 22, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000018048.42

Allele description

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]
Observations:
1

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000038327OMIM
no assertion criteria provided
Pathogenic
(May 1, 1998)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000914705Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Pathogenic
(Dec 19, 2018)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV001499824Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 21, 2021)
maternalclinical testing

PubMed (10)
[See all records that cite these PMIDs]

SCV002012437St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)
Pathogenic
(Oct 28, 2021)
germlineclinical testing

Citation Link,

SCV002580798MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Feb 22, 2022)
germlineclinical testing

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

SCV002587792Wangler Lab, Baylor College of Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

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

SCV002764685Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
criteria provided, single submitter

(Classification criteria August 2017)
Pathogenic
(Aug 17, 2020)
germlineclinical testing

Citation Link,

SCV003841218Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownyes1not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
Caucasiansmaternalyes21not providednot providednot providedclinical testing

Citations

PubMed

Physiological consequences of defects in ERCC1-XPF DNA repair endonuclease.

Gregg SQ, Robinson AR, Niedernhofer LJ.

DNA Repair (Amst). 2011 Jul 15;10(7):781-91. doi: 10.1016/j.dnarep.2011.04.026. Epub 2011 May 25. Review.

PubMed [citation]
PMID:
21612988
PMCID:
PMC3139823

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]
PMID:
24728327
PMCID:
PMC3984285
See all PubMed Citations (13)

Details of each submission

From OMIM, SCV000038327.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

For discussion of the arg788-to-trp (R788W) mutation in the ERCC4 gene that was found in compound heterozygous state in a patient with xeroderma pigmentosum type F (XPF; 278760) by Sijbers et al. (1996), see 133520.0001.

Sijbers et al. (1998) found the R788W mutation in homozygous state in a second Caucasian patient with XPF. Mild ocular photophobia had been present from childhood, and acute skin reactions occurred upon exposure to sunlight. Basal and squamous cell carcinomas developed after his twenty-seventh year. In his late forties, progressive neurologic symptoms emerged, which included intellectual decline, mild chorea and ataxia, and marked cerebral and cerebellar atrophy. Sijbers et al. (1998) stated that such neurologic abnormalities were unusual in XPF, having been described in only 1 of 17 other XPF individuals. The patient's 5-fold reduced activity of nucleotide excision repair in cultured cells, combined with moderately affected cell survival and DNA replication after UV exposure, was typical of XPF. Biochemical, genetic, and clinical data indicated the presence of considerable residual repair activity, strongly suggesting that the R788W mutation is leaky. The 2 Caucasian patients carrying this mutation were not known to be related.

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

From Illumina Laboratory Services, Illumina, SCV000914705.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Across a selection of the available literature, the ERCC4 c.2395C>T (p.Arg799Trp) variant has been identified in 11 probands with xeroderma pigmentosum including five in a homozygous state, four in a heterozygous state and two in a compound heterozygous state (Sijbers et al. 1996; Sijbers et al. 1998; Gregg et al. 2011). The p.Arg799Trp variant is reported at a frequency of 0.001 in the European American population of the Exome Sequencing Project. Functional rescue studies showed that the variant could only partially rescue the nuclear excision repair defect and that the variant protein mislocalized to the cytoplasm (Sijbers et al. 1998; Ahmad et al. 2010). Based on the collective evidence, the p.Arg799Trp variant is classified as pathogenic for xeroderma pigmentosum. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

From Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN, SCV001499824.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasians2not providednot providedclinical testing PubMed (10)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providedbloodnot provided2not provided1not provided

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV002012437.2

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

Description

The ERCC4 c.2395C>T (p.Arg799Trp) missense change has a maximum subpopulation frequency of 0.081% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/16-14041848-C-T). Six of seven in silico tools predict a deleterious effect of this variant on protein function (PP3), and in vitro functional assays in LCLs (Epstein–Barr virus transformed lymphoblastoid cell lines) and fibroblasts have shown that this variant causes reduced protein expression of nuclear ERCC4 which is attributed to protein mislocalization and can result in decreased cell survival and DNA replication after ultraviolet light exposure (PS3; PMID: 20221251, 29105242, 9579555). This variant has been reported in over ten individuals affected with xeroderma pigmentosum (PS4, PM3; PMID: 8797827, 9579555, 23623389, 21228398, 28431612, 29892709). In addition, it has been reported in three individuals with autosomal recessive cerebellar ataxia with mild pigmentation of exposed skin areas and/or an equivocal history of pathological sunburn (PMID: 29403087), one individual with sporadic ataxia (PMID: 31692161), two individuals with head and neck squamous cell carcinoma (PMID: 28678401), one individual with sporadic pancreatic adenocarcinoma (PMID: 28767289), one individual with Cockayne syndrome (PMID: 29105242), and one individual with colorectal cancer (PMID: 31871297). This variant is also known as p.Arg788Trp in the literature. In summary, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP criteria applied: PS3, PS4, PM3, PP3.

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

From MGZ Medical Genetics Center, SCV002580798.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Wangler Lab, Baylor College of Medicine, SCV002587792.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (5)

Description

This missense ERCC4 variant at c.2395C>T (p.R799W) was seen on exome through the Texome project (R01HG011795). This variant has been described in individuals with ERCC4-related conditions (PMID: 8797827, 9579555, 20221251, 27528516). It has been observed in gnomAD with a frequency of 0.040% in the heterozygous state and has not been observed in the homozygous state (PM2). Functional studies suggest this variant is functionally defective (PMID: 9579555, 20221251) (PS3).This variant is predicted to be deleterious (CADD: 31.000) (PP3). The evolutionary conservation of this residue is high. We classify this variant as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV002764685.1

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

From Baylor Genetics, SCV003841218.1

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

Last Updated: Apr 20, 2024