NM_005431.1(XRCC2):c.378_381delACTT (p.Leu126Phefs) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Jan 3, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_005431.1(XRCC2):c.378_381delACTT (p.Leu126Phefs)]

NM_005431.1(XRCC2):c.378_381delACTT (p.Leu126Phefs)

XRCC2:X-ray repair cross complementing 2 [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_005431.1(XRCC2):c.378_381delACTT (p.Leu126Phefs)
  • NC_000007.14:g.152649104_152649107delAAGT
  • NG_027988.1:g.32059_32062delACTT
  • NM_005431.1:c.378_381delACTT
  • NP_005422.1:p.Leu126Phefs
  • NC_000007.13:g.152346189_152346192delAAGT
dbSNP: rs763401560
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_005431.1:c.378_381delACTT - frameshift variant - [Sequence Ontology: SO:0001589]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000569312GeneDxcriteria provided, single submitter
Likely pathogenic
(Jan 3, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000569312.4

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


This deletion of four nucleotides in XRCC2 is denoted c.378_381delACTT at the cDNA level and p.Leu126PhefsX7 (L126FfsX7) at the protein level. The normal sequence, with the bases that are deleted in brackets, is ACTT[delACTT]CTTA. The deletion causes a frameshift which changes a Leucine to a Phenylalanine at codon 126, and creates a premature stop codon at position 7 of the new reading frame. Even though nonsense-mediated decay is not expected to occur, it is significant since the last 155 amino acids are replaced with 6 incorrect amino acids and is predicted to cause loss of normal protein function through protein truncation. This event would result in loss of the Walker B ATPase motif (OÂ’Regan 2001). This variant has not, to our knowledge, been reported in the literature. Based on the currently available information, we consider this deletion to be a likely pathogenic variant.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 17, 2019

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