NM_005431.2(XRCC2):c.789_790del (p.Asn263fs) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 3, 2016
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:: RCV001297351.13

Allele description [Variation Report for NM_005431.2(XRCC2):c.789_790del (p.Asn263fs)]

NM_005431.2(XRCC2):c.789_790del (p.Asn263fs)

Gene:

XRCC2:X-ray repair cross complementing 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q36.1

Genomic location:

Preferred name:

NM_005431.2(XRCC2):c.789_790del (p.Asn263fs)

HGVS:

NC_000007.13:g.152345780_152345781del
NC_000007.14:g.152648696_152648697del
NG_027988.2:g.32470_32471del
NM_005431.2:c.789_790delMANE SELECT
NP_005422.1:p.Asn263fs
LRG_323t1:c.789_790del
LRG_323:g.32470_32471del
LRG_323p1:p.Asn263fs
NC_000007.13:g.152345780_152345781del
NC_000007.13:g.152345780_152345781delTG
NC_000007.13:g.152345781_152345782del
NG_027988.1:g.32470_32471del
NM_005431.1:c.789_790delCA

Protein change:

N263fs

Links:

dbSNP: rs1060502667

NCBI 1000 Genomes Browser:

rs1060502667

Molecular consequence:

NM_005431.2:c.789_790del - 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
SCV001486363	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 3, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001486363

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 3, 2016)

germline

clinical testing

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

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

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, SCV001486363.5

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

Description

Experimental studies have not been reported for this variant and it is currently unknown if the last 18 amino acids of the XRCC2 protein are critical for its function. This sequence change deletes 2 nucleotides from exon 3 of the XRCC2 mRNA (c.789_790delCA), causing a frameshift at codon 263. This creates a premature translational stop signal in the last exon of the XRCC2 mRNA (p.Asn263Lysfs*15). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 18 amino acids of the XRCC2 protein. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in XRCC2 cause disease. Therefore, this variant has been classified as a Variant of Uncertain Significance. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a XRCC2-related disease.

#	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: Oct 20, 2024

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