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NM_000123.4(ERCC5):c.2392G>T (p.Asp798Tyr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 17, 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:
RCV002539589.3

Allele description [Variation Report for NM_000123.4(ERCC5):c.2392G>T (p.Asp798Tyr)]

NM_000123.4(ERCC5):c.2392G>T (p.Asp798Tyr)

Genes:
BIVM-ERCC5:BIVM-ERCC5 readthrough [Gene - HGNC]
LOC126861834:BRD4-independent group 4 enhancer GRCh37_chr13:103518038-103519237 [Gene]
ERCC5:ERCC excision repair 5, endonuclease [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q33.1
Genomic location:
Preferred name:
NM_000123.4(ERCC5):c.2392G>T (p.Asp798Tyr)
HGVS:
  • NC_000013.11:g.102866704G>T
  • NG_007146.1:g.25881G>T
  • NG_086332.1:g.1117G>T
  • NM_000123.4:c.2392G>TMANE SELECT
  • NM_001204425.2:c.3754G>T
  • NP_000114.2:p.Asp798Tyr
  • NP_000114.3:p.Asp798Tyr
  • NP_001191354.2:p.Asp1252Tyr
  • LRG_464t1:c.2392G>T
  • LRG_464:g.25881G>T
  • LRG_464p1:p.Asp798Tyr
  • NC_000013.10:g.103519054G>T
  • NM_000123.3:c.2392G>T
Protein change:
D1252Y
Links:
dbSNP: rs755253596
NCBI 1000 Genomes Browser:
rs755253596
Molecular consequence:
  • NM_000123.4:c.2392G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001204425.2:c.3754G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003442188Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jun 17, 2022)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Pellagra-like condition is xeroderma pigmentosum/Cockayne syndrome complex and niacin confers clinical benefit.

Hijazi H, Salih MA, Hamad MH, Hassan HH, Salih SB, Mohamed KA, Mukhtar MM, Karrar ZA, Ansari S, Ibrahim N, Alkuraya FS.

Clin Genet. 2015;87(1):56-61. doi: 10.1111/cge.12325. Epub 2013 Dec 20.

PubMed [citation]
PMID:
24354460

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003442188.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This missense change has been observed in individuals with clinical features of Cockayne syndrome (PMID: 24354460). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 798 of the ERCC5 protein (p.Asp798Tyr).

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

Last Updated: Sep 29, 2024